NAMIC Wiki - User contributions [en]

NAMIC Wiki:DTI:DICOM for DWI and DTI

2022-12-20T03:23:51Z

Hjmjohnson: /* Related Links */

This page should serve as a place where information about DICOM and DWI/DTI data can be maintained. With time, this information could be used as part of automated solutions for learning all the necessary DWI-related information from a DICOM series. A collection of tools for DICOM is [[DICOM|here]].

As long DICOM support for DWI information is vendor-specific and/or non-conformant with the info here, the [[NAMIC_Wiki:DTI:Nrrd_format|Nrrd format ]] provides a means of recording the DWI-specific information once it is known.

== DICOM for DWI ==

The recommended tags to use in DICOM are as follows:

0018 9075 CS 1 Diffusion Directionality
0018 9076 SQ 1 Diffusion Gradient Direction Sequence
0018 9087 FD 1 Diffusion b-value
0018 9089 FD 3 Diffusion Gradient Orientation
0018 9117 SQ 1 MR Diffusion Sequence
0018 9147 CS 1 Diffusion Anisotropy Type
0018 9602 FD 1 DiffusionBValueXX
0018 9603 FD 1 DiffusionBValueXY
0018 9604 FD 1 DiffusionBValueXZ
0018 9605 FD 1 DiffusionBValueYY
0018 9606 FD 1 DiffusionBValueYZ
0018 9607 FD 1 DiffusionBValueZZ

These are defined in [ftp://medical.nema.org/medical/dicom/final/sup49_ft.pdf Supplement 49]. In particular see section C.8.12.5.9 "MR Diffusion Macro" on pages 94 and 95.

The tags are also referenced in http://medical.nema.org/dicom/2004/04_06PU.PDF (see pages 28-29) as well as in some [http://medical.nema.org/Dicom/minutes/WG-07/WG-07_2005/Minutes-2005-10-20-21-Denver.doc Working Group Minutes] (see pages 155-156).

Two points of interest relative to the NRRD format:

* The definition of "Diffusion Gradient Orientation" implies that the measurement frame is exactly the identity transform.
* While one can encode the B-matrix, it is [https://github.com/rordenlab/dcm2niix/issues/265 underspecified to store the polarity of the b-vector]. This makes it insufficient for tools like [https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/eddy#eddy_--_a_tool_for_correcting_eddy_currents_and_movements_in_diffusion_data FSL's eddy] which leverage the fact that polar opposite b-vectors should have identical true signal yet differ due to eddy currents (and therefore artifacts can be modeled and removed).

=== Private vendor: Canon ===

For Canon (né Toshiba) scanners saving classic 2D DICOM images, the gradient direction is stored in the text-based image comments fields. For older systems, the DiffusionBValue (0018,9087) tag may be omitted for images where the b-value is equal to zero. Be aware that the gradient direction stored in the comment field may not take into account the phase encoding polarity, so it may not be accurate. Example data illustrating this problem is [https://github.com/neurolabusc/dcm_qa_canon available]. For this reason, one should concern using a tool like GradFlipTest to determine the gradient direction. A sample for this type of data might be:

* (0018,9087) FD 1500 # 8, 1 DiffusionBValue
* (0020,4000) LT [b=1500(0.445,0.000,0.895)] # 26, 1 ImageComments

When Canon scanners save data as enhanced DICOM, public tags (0018,9087; 0018,9089) are used. [https://github.com/neurolabusc/dcm_qa_canon Exemplars] suggest that gradient direction is specified correctly regardless of phase encoding polarity.
* (0018,9087) FD 1500 # 8, 1 DiffusionBValue
* (0018,9089) FD 0.29387456178665161\-0.95365142822265625\-0.064700603485107422 # 24, 3 DiffusionGradientOrientation

=== Private vendor: GE ===

For GE scanners, Signa Excite 12.0 and later, the following tags are reserved for diffusion weighted images:

* (0019,10e0) : # DTI diffusion directions (release 10.0 & above)
* (0019,10df) : # DTI diffusion directions (release 9.0 & below)
* (0019,10d9) : Concatenated SAT {# DTI Diffusion Dir., release 9.0 & below}
* (0021,105A) : diffusion direction
* (0043,1039) : Slop_int_6... slop_int_9: (in the GEMS_PARM_01 block)
** 6: b_value
** 7: private imaging options 2
** 8: ihtagging
** 9: ihtagspc

This information can be found in http://www.gehealthcare.com/usen/interoperability/dicom/docs/5162373r1.pdf

Unfortunately the [[DataRepository|Dartmouth DWI data ]] (from a GE Signa scanner) does not conform to this (nor do they use the nominally standard 0x0018 tags), as can be seen by running:

dcdump S4.100 | & grep \(0x0019,0x10

which includes:

(0x0019,0x10d9) DS Concatenated SAT VR=<DS> VL=<0x0008> <0.000000>
(0x0019,0x10df) DS User Data VR=<DS> VL=<0x0008> <0.000000>
(0x0019,0x10e0) DS User Data VR=<DS> VL=<0x0008> <0.000000>

so all of the tags which are supposed to store # gradient directions store the value 0! In addition, there is:

(0x0021,0x105a) SL Integer Slop VR=<SL> VL=<0x0004> [0x00000000]

so the supposed representation of diffusion-direction is also empty. The Dartmouth data has the following tags describing the scanner and software version:

(0008,1090) LO [GENESIS_SIGNA]
(0018,1020) LO [09]

In GE DWI images (software version 12.0)

(0008,1090) LO [SIGNA EXCITE]
(0018,1020) LO [12\LX\MR Software release:12.0_M4_0520.a]

diffusion directions are stored under the following tags:

(0019,10bb) DS [0.430617]
(0019,10bc) DS [-0.804161]
(0019,10bd) DS [-0.420008]

these directions are in the image (rather than scanner bore) frame of reference. The interpretation depends on the Phase Encoding direction (0018,1312). If 0018,1312 is "COL" than 0019,10bb refers to the image columns (i), 0019,10bc refers to the image rows (j) and 0019,10bd refers to the slices (k). If 0018,1312 is "ROW" than 0019,10bb refers to the image rows (j), 0019,10bc refers to the image columns (i) and 0019,10bd refers to the slices (k). There are two caveats: first this assumes that your slices are stacked in spatially ascending order (head to foot for axial acquisitions) regardless of the order that they were saved to disk (which appears to vary depending on how the user plans the scan). Second, you need to adjust the polarity of these directions to match the expectations of the software used for fitting.

Be aware that the b_value stored in tag 0043,1039 may be masked. For example, consider [https://github.com/nikadon/cc-dcm2bids-wrapper/tree/master/dicom-qa-examples/ge-mr750-dwi-b-vals#table series 16] from this archive. This series has images with b_values of both 750 and 1500, but the DICOM tag stores b_values of 1000001500 and 1000000750, as shown in the DICOM dump from image 24 (below). Therefore, if you use 0043,1039 to determine b_value, you should use the modulus of a large number like 100,000.

(0043,1039) IS [1000001500\8\0\0]

=== Private vendor: Siemens ===

Siemens software is reported by Series, Generation, Major Version and Minor Version. Therefore, 'VB17' data was created on a V-series, B-generation, version 1.7. Historically, all Siemens systems were V-series (Trio, Skyra, Prisma, etc), so people might just say data was from 'B17'.

For Siemens V-series systems from the B-generation onward (around 2005), the most reliable way to read diffusion gradients is from the [https://nipy.org/nibabel/dicom/siemens_csa.html CSA header]. Specially, for the 'DiffusionGradientDirection' and 'B_value' tags.

For the X-series (e.g. Vida and Sola, XA10 and XA11) systems will use the recommended public tags (described above) when exporting as enhanced DICOM. Therefore, the relevant DICOM data for Siemens X-series might look like this:

(0019,100c) IS [10] # 2,1 B_value
(0019,100d) CS [BMATRIX ] # 8,1 DiffusionDirectionality
(0019,100e) FD -0.57735\0.57735\0.57735 # 24,3 DiffusionGradientDirection
(0019,1027) FD 3\-3\-3\3\3\3 # 48,6 B_matrix

=== Private vendor: Siemens (Historical) ===

The data below is useful for older Siemens equipment (software ~2005 or earlier).

A Siemens DICOM Conformance Statement is available at

http://www.medical.siemens.com/siemens/en_INT/rg_marcom_FBAs/files/brochures/DICOM/mr/dcs_trio.pdf

No diffusion related tags specified.

David Tuch has stated (in email from December 21, 2005):

The diffusion gradient information and coordinate frame are not provided
in the DICOM hdr for the MGH diffusion sequences.

'''Tag 0029,1010''' may include all necessary information

If you have installed spm (and Matlab), the following spm-File extracts the gradient info:

P= spm_get(Inf,'*','Selct some files')
hdr=spm_dicom_headers(P)
hdr{1}.CSAImageHeaderInfo(22).item(1).val
hdr{1}.CSAImageHeaderInfo(22).item(2).val
hdr{1}.CSAImageHeaderInfo(22).item(3).val

look for "spm_dicom_headers.m" (google or on your hard disk), this spm File shows you how to decode the tag data.

It is easy to write a C or C++ program that does the same, if you have the spm_dicom_headers.m

Credits: Jan Klein <klein AT mevis DOT de>

==== Update ====

<br /> As far as the latest MR scanner software (2006) version is concerned, a solution for the access of the following Diffusion attributes was provided:

0019;000A;SIEMENS MR HEADER ;NumberOfImagesInMosaic ;1;US;1
0019;000B;SIEMENS MR HEADER ;SliceMeasurementDuration ;1;DS;1
0019;000C;SIEMENS MR HEADER ;B_value ;1;IS;1
0019;000D;SIEMENS MR HEADER ;DiffusionDirectionality ;1;CS;1
0019;000E;SIEMENS MR HEADER ;DiffusionGradientDirection ;1;FD;3
0019;000F;SIEMENS MR HEADER ;GradientMode ;1;SH;1
0019;0027;SIEMENS MR HEADER ;B_matrix ;1;FD;6
0019;0028;SIEMENS MR HEADER ;BandwidthPerPixelPhaseEncode ;1;FD;1

That does not solve your problem with the older datasets and unfortunately there is no easy way to access diffusion information there as it is really only stored in the Siemens shadow part.

==== Update September 2010 ====

Via email, Matthew Brett reported the following information and links which are posted here with his permission.

<pre>
...if you do this:

P= spm_get(Inf,'*','Selct some files')
hdr=spm_dicom_headers(P)
hdr{1}.CSAImageHeaderInfo(22).item(1).val
hdr{1}.CSAImageHeaderInfo(22).item(2).val
hdr{1}.CSAImageHeaderInfo(22).item(3).val

from http://www.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI#Private_vendor:_Siemens

- then the resulting q-like vectors can be rather far off, for reasons
that I now can't remember, but I believe Guy investigated.

In SPM, hdr{1}.CSAImageHeaderInfo is the SPM reading of the Siemens
private header. We read this in:

http://github.com/matthew-brett/nibabel/blob/master/nibabel/nicom/csareader.py

in the 'read' function.

What SPM calls hdr{1}.CSAImageHeaderInfo(22) has the label
'DiffusionGradientDirection', and is what looks like the q-vector.
However, it can be rather far off, and, in particular, is often rather
far from a unit vector.

Guy recovered from this by using the correctly specified 'B_matrix'
field of the same private header. I think this is:

hdr{1}.CSAImageHeaderInfo(78)

in SPM-speak, and is arranged as (0-based matrix indices into B matrix)

(0,0), (0, 1), (0,2), (1, 1), (1, 2), (2, 2)

where the B matrix is symmetric. See 'get_b_matrix' in

http://github.com/matthew-brett/nibabel/blob/master/nibabel/nicom/csareader.py

We (this is obviously optional) rotate to voxel orientation (rather
than DICOM orientation).

We (this is also optional) (credit Ian Nimmo-Smith) resolve to the
nearest positive semi-definite matrix using Niethammer's and C-Fs
tensor algorithm - see 'nearest_pos_semi_def' in:

http://github.com/matthew-brett/nibabel/blob/master/nibabel/nicom/dwiparams.py

Finally, we extract the best estimate of q from the resulting B
matrix, using eigenvalue decomposition - see 'B2q' in the dwiparams -
this is the main part of Guy's algorithm, and Ian N-S code.

But I think you're asking - can I put that on the NAMIC page?

I'm hoping that Guy or Ian or Eleftherios will jump in and tell me
where I am wrong or explain further...

</pre>

This bug may or may not be related (now fixed): http://www.na-mic.org/Bug/view.php?id=978

==== Reference ====

* http://www.mmrrcc.upenn.edu/CAMRIS/cfn/

in particular:

* http://www.mmrrcc.upenn.edu/CAMRIS/cfn/dicomhdr.html

=== Private vendor: Philips ===

Be aware that Philips will store derived diffusion images (e.g. isotropic images) in the same series as the raw data. Derived images will disrupt processing. Further, one will be able to generate better derived images after processing (e.g. de-Gibbs, de-noise, eddy correction). Therefore, one typically wants to identify and discard these derived images.

Many Philips images use the following private tags for diffusion weighted images

* (2001,1003) FL : Diffusion B-Factor
* (2001,1004) CS : Diffusion Direction
* (2005,10B0) FL : Diffusion Direction RL
* (2005,10B1) FL : Diffusion Direction AP
* (2005,10B2) FL : Diffusion Direction FH

Note that the [http://incenter.medical.philips.com/doclib/enc/fetch/2000/4504/577242/577256/588723/5144873/5144488/5144982/DICOM_Conformance_Statement_Ingenia_R4.1.pdf%3fnodeid%3d8124182%26vernum%3d-2 possible values for 2001,1004] are P (PreparationDirection), M (MeasurementDirection), S (Selection Direction),O(Oblique Direction), I (Isotropic). Since both the raw B=0 images and derived isotropic use the value "I" this tag is insufficient to discriminate raw images from derived images. For Philips scans, B=0 set all tags 2001,1003; 2005,10B0; 2005,10B1 and 2005,10B2 to zero, while derived images use the corresponding b-value (e.g. 2001,1003 = 1000) but set also set 2001,10B0; 2005,10B1; 2005,10B2 to zero. Raw B-weighted images have a positive value in 2001,1003 and at least one of the gradient directions 2001,10B0; 2005,10B1; 2005,10B2 will be non-zero.

Some Philips images use the recommended public tags described above (for example classic DICOM images from 2012 where 0002,0013 lists Philips MR 26.2 as well as 2018-vintage Philips MR 53.0). Philips enhanced DICOMs also use these public tags.

Complete DICOM conformance statements for

* Intera
* Achieva
* Panorama
* Gyroscan
* Infinion / Eclipse

are available here http://www.medical.philips.com/main/company/connectivity/mri/

=== Private vendor: Toshiba ===

The Toshiba Titan 3T (console software V2.30*R005) uses a standard DICOM attribute for b-value:
* (0018,9087) : Diffusion b-value (for instances with a non-zero b-value).
NOTE: this attribute is missing for those instances with a b-value of zero.

Gradients can be found in a private tag as follows:
* (0029, 1001) : Private Sequence
* >(0029, 1090): Private Byte Data
When the byte data is reversed and the nybble-pairs are swapped, this becomes a DICOM sequence object (with 6 items). The 5th item contains a number of standard DICOM attributes including:
* >>(0018,9087) : Diffusion b-value (which matches the above)
* >>(0018,9089) : Diffusion Gradient Orientation. This is the diffusion direction and will be [0, 0, 0] for the b-value of zero instances.

Sample code for the byte data adjustment:
<pre>
private static byte[] adjustToshibaBytes( byte[] input ) {
int len = input.length;
byte[] output = new byte[ len ];
for( int i = 0; i < len; i++ )
{
output[ i ] = (byte)((input[ len - i - 1 ] & 0x0F) + (input[ len - i - 1 ] & 0xF0));
}
return output;
}
</pre>

=== Private vendor: UIH ===

United Imaging Healthcare ("UIH") MRI scanners generate a number of [https://github.com/rordenlab/dcm2niix/tree/master/UIH private tags]. For Diffusion imaging, the crucial ones are the b-value and gradient direction.

(0065,1009) FD 929.75018313375267 # 8, 1 B_value
(0065,1037) FD 0.219573072677\0.9618\0.1632 # 24, 3 DiffusionDirectionality

== DICOM for estimated diffusion tensors ==

There is no specification right now in DICOM to support Tensor. Only a supplement:

[ftp://medical.nema.org/medical/dicom/supps/sup63_pc.pdf Supp 63 Parts 3,4,5,6,16,17 Multi-dimensional Interchange Object ]

The discussion would then be (D. Clunie quote):

Indeed, even if one were to try to standardize in DICOM the encoding
of the entire diffusion tensor, there would no doubt be considerable
debate as to whether to do that as 6 (or 9) planes of an "image", since
there is such a matrix at each spatial location ("pixel"), or as
a special case of the proposed Sup 63 object; the former would keep
image-oriented tools and software happier, the latter would require
implementing a new mechanism and navigating through a more general
structure.

== Validation Datasets ==

Sample datasets are available for most manufacturers that provide concrete examples for their storage of diffusion information:

* [https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage#Diffusion_Tensor_Imaging dcm2niix NITRC page includes GE, Philips and Siemens DICOMs]
* [https://github.com/neurolabusc/dcm_qa_canon_enh Canon Classic DICOMs]
* [https://github.com/neurolabusc/dcm_qa_canon_enh Canon Enhanced DICOMs]
* [https://github.com/neurolabusc/dcm_qa_philips Philips DICOMs]
* [https://osf.io/brvak/ Siemens Mosaic DICOMs]
* [https://github.com/neurolabusc/dcm_qa_uih UIH DICOMs]

== Related Links ==

[http://www.na-mic.org/Wiki/index.php/NAMIC_Tools_Suite_for_DTI_analysis 2010 Project week: NAMIC tools for DTI analysis ]

[http://www.na-mic.org/Wiki/index.php/Projects:DicomToNrrdForDTI DicomToNrrdForDTI Notes]

[http://www.na-mic.org/Wiki/index.php/DTI:Acquisition Randy's DTI Acquisition notes]

== Python psuedocode ==

```python

def get_bvalue(dicom_header_info) -> str:
"""
Extract bvalue from pydicom information
`dicom_header_info = dicom.read_file(dicom_file_name, stop_before_pixels=True)`
:param dicom_header_info: A pydicom object
:return: a string representing the BValue
"""
# bvalue tags from private fields provided by https://www.nmr.mgh.harvard.edu/~greve/dicom-unpack
private_tags_map = {
"Standard": (0x0018, 0x9087),
"UHI": (0x0065, 0x1009),
"GE": (0x0043, 0x1039),
"Siemens": (0x0019, 0x100C),
"Siemens_historical": (0x0029, 0x1010), # NOT SUPPORTED
"Siemens_old": (0x0019, 0x000C),
"Philips": (0x2001, 0x1003)
# "Toshiba" : # Uses (0x0018, 0x9087) standard
}
for k, v in private_tags_map.items():
if v in dicom_header_info:
# This decoding of bvalues follows the NAMIC conventions defined at
# https://www.na-mic.org/wiki/NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI
dicom_element = dicom_header_info[v]
if k == "GE":
large_number_modulo_for_GE = 100000
value = dicom_element.value[0] % large_number_modulo_for_GE
elif dicom_element.VR == "OB":
value = dicom_element.value.decode("utf-8")
else:
value = dicom_element.value
print(f"Found BValue at {v} for {k}, {value} of type {dicom_element.VR}")
return str(value)
return "-1234"
```

2015 Winter Project Week:VersorTransforms

2015-01-09T16:39:47Z

Hjmjohnson: /* Project Description */

__NOTOC__
<gallery>
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==

* Bradley Lowekamp (MSC/NLM)
* Han Johnson (University of Iowa)?

==Project Description==

The ITK transforms ScaleSkewVersor3D, and Simularity3D surprisinging use addition to compose the matrix components instead of matrix multiplication.

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Determine if this is expected and known behavior, and determine if the expected transforms are needed.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
*
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Discussed the issue
* Determined that documentation is needed to clearly describe what is being done to preserve backwards compatibility. Changing the current implementation is too intrusive. New composite transform based transforms should be created to provide a more correct solution.

</div>
</div>

2014 Summer Project Week:UpdateBRAINSTools

2014-06-27T13:09:54Z

Hjmjohnson: /* Project Description */

__NOTOC__
<gallery>
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]
Image:SlicerDWIConvert.png|[[GUI|Slicer GUI]]
</gallery>

==Key Investigators==
* IOWA: Hans, Dave, Kent
* Kitware: JC
* NLM: Brad
* Various NAMIC team members

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Update Slicer build to include BRAINSTools based on ITKv4 registration framework
* Ensure all BRAINSTools regression tests pass in the Slicer environment
* Test ITK thread pool implementation in Slicer build
* ITKv4 registation in SimpleITK

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Write Tests, Write Code, Drink Coffee, Sleep (Optional)
* Repeat
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Create new GUI layout for DWIConvert based on user feedback (Thanks Sonia!)
* Successfully update nightly BRAINSTools in Slicer
** Now using the ITKv4 registration framework
** Update Slicer to ITK release candidate.
*Convert Toews Feat
** Put it in github
** Convert image IO to ITK
** Convert Transform formats to ITK compliant
** Convert command line interface to SlicerExecutionModel
** Compliant with ITK Image and ITK Transform file interfaces.
</div>
</div>

2014 Summer Project Week:UpdateBRAINSTools

2014-06-27T12:56:30Z

Hjmjohnson: /* Key Investigators */

2014 Summer Project Week:UpdateBRAINSTools

2014-06-27T12:55:25Z

Hjmjohnson:

File:SlicerDWIConvert.png

2014-06-27T12:54:19Z

Hjmjohnson: Image for Summer Project Week 2014

Image for Summer Project Week 2014

2014 Summer Project Week:UpdateBRAINSTools

2014-06-27T12:52:49Z

Hjmjohnson:

__NOTOC__
<gallery>
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]
Image:
</gallery>

==Key Investigators==
* IOWA: Hans, Dave, Kent
* Kitware: JC
* NLM: Brad

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Update Slicer build to include BRAINSTools bbased on ITKv4 registation fravework
* Ensure all BRAINSTools regression tests pass in the Slicer environment
* Test ITK thread pool implemation in Slicer build
* ITKv4 registation in SimpleITK

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
*
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

2014 Project Week:DWIConverter

2014-01-10T16:20:27Z

Hjmjohnson:

[[File:Screen Shot 2014-01-10 at 9.10.46 AM.png]]

==Key Investigators==
* Iowa: Hans Johnson
* Kitware: JC
* Slicer: Steve

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
Fix bug [[://www.na-mic.org/Bug/view.php?id=3544|3544]] where Slicer CLI interface and DWIConvert are not passing the converted .nrrd file to the interface.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* [HANS - [*DONE*] Create failing test case
** Command line converts correctly, and resulting DWI image loads in Slicer
** GUI module claims success, but resulting DWI image is never loaded in Slicer
* Identify problem
** [JC/Steve/Hans --[*DONE*] Sit and debug UKF
** [KENT -- Wednesday] Fix bug
* Fix
** [KENT--[*DONE*]] Merge fixed version with BRAINSTools, and then update Slicer to new BRAINSTools with bug fixes.
** [HANS] Create stub documentation page
** [KENT] Add details to documentation page.
** [All] CELEBRATE!

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
** [DONE --not needed] Test case completed, need to push to common location.

</div>
</div>

2014 Project Week:DWIConverter

2014-01-10T16:15:29Z

Hjmjohnson:

[[File:Screen Shot 2014-01-10 at 9.10.46 AM.png]]

[[File:Screen Shot 2014-01-10 at 9.04.27 AM.png]]

==Key Investigators==
* Iowa: Hans Johnson
* Kitware: JC
* Slicer: Steve

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
Fix bug [[://www.na-mic.org/Bug/view.php?id=3544|3544]] where Slicer CLI interface and DWIConvert are not passing the converted .nrrd file to the interface.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* [HANS - DONE] Create failing test case
** Command line converts correctly, and resulting DWI image loads in Slicer
** GUI module claims success, but resulting DWI image is never loaded in Slicer
* Identify problem
** [JC/Steve/Hans -- Wednesday] Sit and debug
** [KENT -- Wednesday] Fix bug
* Fix
** [KENT--Thusday] Merge fixed version with BRAINSTools, and then update Slicer to new BRAINSTools with bug fixes.
** [HANS] Create stub documentation page
** [KENT] Add details to documentation page.
** [All] CELEBRATE!

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
** Test case completed, need to push to common location.

</div>
</div>

File:Screen Shot 2014-01-10 at 9.10.46 AM.png

2014-01-10T16:12:02Z

Hjmjohnson:

File:Screen Shot 2014-01-10 at 9.04.27 AM.png

2014-01-10T16:05:17Z

Hjmjohnson: Screen shot of bug fix.

Screen shot of bug fix.

File:20140110 IowaDBPProgress.pdf

2014-01-09T16:23:03Z

Hjmjohnson: 2014 AHM Huntington's Disease Progress Report.

2014 AHM Huntington's Disease Progress Report.

2014 Project Week:DWIConverter

2014-01-06T17:34:17Z

Hjmjohnson: Created page with '==Key Investigators== * Iowa: Hans Johnson * Kitware: JC * Slicer: Steve ==Project Description== <div style="margin: 20px;"> <div style="width: 27%; float: left; padding-right:…'

==Key Investigators==
* Iowa: Hans Johnson
* Kitware: JC
* Slicer: Steve

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
Fix bug [[://www.na-mic.org/Bug/view.php?id=3544|3544]] where Slicer CLI interface and DWIConvert are not passing the converted .nrrd file to the interface.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* [HANS - DONE] Create failing test case
** Command line converts correctly, and resulting DWI image loads in Slicer
** GUI module claims success, but resulting DWI image is never loaded in Slicer
* Identify problem
** [JC/Steve/Hans -- Wednesday] Sit and debug
** [KENT -- Wednesday] Fix bug
* Fix
** [KENT--Thusday] Merge fixed version with BRAINSTools, and then update Slicer to new BRAINSTools with bug fixes.
** [HANS] Create stub documentation page
** [KENT] Add details to documentation page.
** [All] CELEBRATE!

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
** Test case completed, need to push to common location.

</div>
</div>

2014 Project Week:Modules scripting

2014-01-06T17:06:33Z

Hjmjohnson: Created page with '==Key Investigators== * Iowa: David Welch * NLM: Brad Lowekamp * Iowa: Hans Johnson ==Project Description== <div style="margin: 20px;"> <div style="width: 27%; float: left; pad…'

==Key Investigators==
* Iowa: David Welch
* NLM: Brad Lowekamp
* Iowa: Hans Johnson

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
Enhance the integration of SimpleITK with Slicer and expand the documentation for building modules from SimpleITK
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Enhance the interface for the existing "SimpleFilters" module to allow for label maps and image types to be better handled.
** [BRAD] Explain how the SimpleFilters module works
** [DAVE] Make outputs default to NOT overwriting the inputs
** [DAVE] For binary image outputs, set them as labelmaps

* Convert SimpleITK functions to user interface modules
** [DAVE] Create a SimpleITK function that histogram equalizes one image to another. "outimage=histEQ(refImage,inputImage,numberOfBins)"
** [DAVE] Convert that simple function to a Slicer GUI interface

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>

</div>
</div>

2014 Winter Project Week

2014-01-06T16:55:24Z

Hjmjohnson: /* Huntington's Disease */

Back to [[Project Events]], [[AHM_2014]], [[Events]]

__NOTOC__
[[image:PW-SLC2014.png|300px]]

Project Week is a hands on activity -- programming using the open source [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the NA-MIC, NCIGT, and NAC calendars. It is held in the summer at MIT, typically the last week of June, and a shorter version is held in Salt Lake City in the winter, typically the second week of January.

Active preparation begins 6-8 weeks prior to the meeting, when a kick-off teleconference is hosted by the NA-MIC Engineering, Dissemination, and Leadership teams, the primary hosts of this event. Invitations to this call are sent to all NA-MIC members, past attendees of the event, as well as any parties who have expressed an interest in working with NA-MIC. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient NA-MIC coverage for all. Subsequent teleconferences allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams are asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself starts off with a short presentation by each project team, driven using their previously created description, and allows all participants to be acquainted with others who are doing similar work. In the rest of the week, about half the time is spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half is spent in project teams, doing hands-on programming, algorithm design, or clinical application of NA-MIC kit tools. The hands-on activities are done in 10-20 small teams of size 3-5, each with a mix of experts in NA-MIC kit software, algorithms, and clinical. To facilitate this work, a large room is setup with several tables, with internet and power access, and each team gathers on a table with their individual laptops, connects to the internet to download their software and data, and is able to work on their projects. On the last day of the event, a closing presentation session is held in which each project team presents a summary of what they accomplished during the week.

A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].
= Dates.Venue.Registration =

Please [[AHM_2014#Dates_Venue_Registration|click here for Dates, Venue, and Registration]] for this event.

= [[AHM_2014#Agenda|'''AGENDA''']] and Project List=

Please:
* [[AHM_2014#Agenda|'''Click here for the agenda for AHM 2014 and Project Week''']].
* [[#Projects|'''Click here to jump to Project list''']]

=Background and Preparation=

A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].

Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]

=Projects=
* [[2014_Project_Week_Template | Template for project pages]]

==TBI==
*[[2014_Project_Week:TBIatrophy|Multimodal neuroimaging for the quantification of brain atrophy at six months following severe traumatic brain injury]] (Andrei Irimia, SY Matthew Goh, Carinna M. Torgerson, John D. Van Horn)
*[[2014_Project_Week:TBIdemyelination|Systematic evaluation of axonal demyelination subsequent to traumatic brain injury using structural T1- and T2-weighted magnetic resonance imaging]] (Andrei Irimia, SY Matthew Goh, Carinna M. Torgerson, John D. Van Horn)
*[[2014_Project_Week:BrainAging|Mapping the effect of traumatic brain injury upon white matter connections in the human brain using 3D Slicer]] (Andrei Irimia, John D. Van Horn)
*[[2014_Project_Week:LongitudinalDTI|Patient-specific longitudinal DTI analysis in traumatic brain injury]] (Anuja Sharma, Andrei Irimia, Bo Wang, John D. Van Horn, Martin Styner, Guido gerig)
*[[2014_Project_Week:TBISegmentation|Testing the interactive segmentation algorithm for traumatic brain injury]] (Bo Wang, Marcel Prastawa, Andrei Irimia, John D. Van Horn, Guido Gerig)

==Atrial Fibrillation==
*[[2014_Project_Week:MRAFusionRegistration|DEMRI LA Segmentation via Image Fusion (MRA)]] (Josh, Salma, Alan)
*[[2014_Project_Week:LAFibrosisVisualizationModule|LA Fibrosis / Scar Visualization]] (Josh, Salma, Alan)
*[[2014_Project_Week:CARMADocumentation|CARMA Extension Documentation Project]] (Josh, Salma)
*[[2014_Project_Week:GraphCutsLASegmentationModule|LA Segmentation module using multi-column Graph Cuts]] (Gopal, Salma, Josh, Rob, Ross)
*[[2014_Project_Week:JointImageAndShapeAnalysisForFibrosisDistribution|Joint Image and Shape Analysis for Fibrosis Distribution]](Yi Gao, LiangJia Zhu, Josh Cates, Rob MacLeod, Sylvain Bouix, Ron Kikinis, Allen Tannenbaum)
*[[2014_Project_Week:GrowCutLevelSetLA|Grow cut, level set integration for interactive LA segmentation]] ( Liangjia Zhu, Ivan Kolesov, Yi Gao, Allen Tannenbaum)

==Huntington's Disease==
*[[2014_Project_Week:DWIDispersion|DWI Dispersion & Compressed Sensing Conversions]] (Hans, CF, Peter Savadjiev, Kent, David)
*[[2014_Project_Week:Modules scripting|Slicer module scripting?]] (David)
*[[2014_Project_Week:DWIConverter|DWIConverter?]] (Hans, Kent)
*[[2014_Project_Week:Slicer_Based_Surface_Template_Estimation|Slicer Based Surface Template Estimation]] (Saurabh Jain, Steve Pieper, Hans Johnson, Josh Cates)
*[[2014_Project_Week:HD_4DShapes|4D shape analysis: application to HD ]] (James Fishbaugh,Hans Johnson, Guido Gerig)
*[[2014_Project_Week:Shape_Registration_and_Regression|Shape registration and regression in Slicer4 ]] (James Fishbaugh,Hans Johnson, Guido Gerig)

==Head and Neck Cancer==
*[[2014_Project_Week:DIR_validation|DIR Validation]] (Nadya and Greg)
*[[2014_Project_Week:Hybrid_bspline|Hybrid B Spline]] (Nadya, Greg, Steve)
*[[2014_Project_Week:CarreraSlice|Interactive Segmentation]] (Ivan, LiangJia, Nadya, Yi, Greg, Allen)

==Slicer4 Extensions==
*[[2014_Project_Week:ShapePopulationViewer|Surface Visualization - ShapePopulationViewer]] (Alexis Girault, Francois Budin, Beatriz Panaigua, Martin Styner)
*[[2014_Project_Week:DTIAnalysisPipeline|DTI Analysis Pipeline as Slicer4 Extensions]] (Francois Budin, Martin Styner)

==Cardiac==
*[[2014_Project_Week:CardiacStemCellMonitoring|Monitoring engrafted stem cells in cardiac tissue with time series manganese enhanced MRI]] (Karl Diedrich)
*[[2014_Project_Week:CardiacCongenitalSegmentation|Whole-heart segmentation of cardiac MR images in congenital heart defect cases]] (Danielle Pace, Polina Golland)

==Stroke==

*[[2014_Project_Week:Multi-Tissue_Stroke_Segmentation|Multi-Tissue Stroke Segmentation]] (Ramesh, Polina B., Polina G.)

==Brain Segmentation==
*[[2014_Project_Week:MultiAtlas_MultiImage_Segmentation|Multi-Atlas based Multi-Image Segmentation]] (Minjeong Kim, Xiaofeng Liu, Jim Miller, Dinggang Shen)

==Image-Guided Interventions==
*[[2014_Project_Week:OpenIGTLink| OpenIGTLink Interface: New data types and structures]] (Junichi Tokuda, Andras Lasso, Steve Piper, ???)
*[[2014_Project_Week:Ultrasound Visualization and Navigation in Neurosurgery|Ultrasound Visualization and Navigation in Neurosurgery]] (Matthew Toews, Alireza Mehrtash, Csaba Pinter, Andras Lasso, Steve Pieper, William M. Wells III)
*[[2014_Project_Week:PercutaneousApproachAnalysis| Percutaneous Approach Analysis]] (Atsushi Yamada, Junichi Tokuda, Koichiro Murakami, ??)
*[[2014_Project_Week:EndoscopeConsole| Endoscope Console]] (Atsushi Yamada, Junichi Tokuda, ??)
*[[2014_Project_Week:Statistical Shape Model for robotic spine surgery| Statistical Shape Model for robotic spine surgery]] (Marine Clogenson, ???)
*[[2014_Project_Week:ImmersiveVR| Immersive VR devices]] (Franklin King, Andras Lasso)

==Radiation Therapy==
*[[2014_Project_Week:DICOM_RT|DICOM RT Export]] (Greg Sharp, Kevin Wang, others??)
*[[2014_Project_Week:DICOM_SRO|DICOM Spatial Registration Export]] (Greg Sharp, Kevin Wang, others??)
*[[2014_Project_Week:Registration_Evaluation|Interactive Registration and Evaluation]] (Kevin Wang, Steve Pieper, Greg Sharp)
*[[2014_Project_Week:External_Beam_Planning|External Beam Planning Visualization]] (Kevin Wang, Greg Sharp, Csaba Pinter)

==TMJ-OA==
* [[2014_Winter_Project_Week:Constrain Fiducial along Suface|Constrain Fiducial along Suface]] (Vinicius Boen, Nicole Aucoin, Beatriz Paniagua)
* [[2014_Winter_Project_Week:Cropping Multiple Surfaces|Cropping multiple surfaces simultaneously]] (Alexander, Jc, Steve, Vinicius, Beatriz Paniagua)
* [[2014_Winter_Project_Week:Color Code Tables|Color Coded Tables]] (Vinicius Boen, Beatriz Paniagua, Nicole Aucoin, Steve Pieper, Francois Budin)
* [[2014_Winter_Project_Week:4DShape Analysis of mandibular changes|4DShape Analysis of mandibular changes]] (Vinicius Boen, James Fishbaugh, Guido Gerig)

==Chronic Obstructive Pulmonary Disease ==
* [[2014_Winter_Project_Week:CIP Core|Chest Imaging Platform (CIP) - Core Infrastructure]] (Raul San Jose, Rola Harmouche, Pietro Nardelli, James Ross)
* [[2014_Winter_Project_Week:CIP Infrastructure Testing and SuperBuild|CIP Testing and SuperBuild]] (James Ross, Raul San Jose)
* [[2014_Winter_Project_Week:Slicer CIP Slicer MRML| Slicer CIP- MRML consolidation]] (Pietro Nardelli, Rola Harmouche, James Ross, Raul San Jose)
* [[2014_Winter_Project_Week:Slicer CIP Modules| Slicer CIP- Modules]] (Rola Harmouche, Pietro Nardelli, James Ross, Raul San Jose)

==[http://qiicr.org QIICR]==

*[[2014_Project_Week:4D_NIfTI_Multivolume|4D NIfTI Multivolume Support]] (Jayashree, Andrey, Jim, John)
*[[2014_Project_Week:RT_FormatConversions|RT and ITK Format Conversions]] (Jayashree, Andras, Csaba. John)
*[[2014_Project_Week:BatchConvertDICOM|Python Scripting Slicer DICOM read/write to convert segmentation objects]] (Jayashree, Andrey, Alireza, Steve, Jc, Hans, John)
*[[2014_Project_Week:PkModeling_user_tool|User module for DCE modeling]] (Andrey, Jayashree, Jim, Alireza, Steve, Ron)
*[[2014_Project_Week:DICOM_enhanced_multiframe|DICOM enhanced multiframe object support]] (Andrey, Alireza, David Clunie, Jayashree, Steve, Reinhard, Jim)
*[[2014_Project_Week:Quantitative_Index_Computation|Quantitative Index Computation]] (Ethan Ulrich, Reinhard Beichel, Nicole, Andrey, Jim)
*[[2014_Project_Week:TCIA Browser Extension in Slicer|TCIA Browser Extension in Slicer]] (Alireza, Andrey, Steve, Ron)

==Infrastructure==
*[[2014_Project_Week:MRMLSceneSpeedUp|MRML Scene speed up]] (Jc, Andras Lasso)
*[[2014_Project_Week:MultidimensionalDataSupport|Multidimensional data support]] (Andras Lasso, Andriy Fedorov, Steve Pieper, JC, Kevin Wang)
*[[2014_Project_Week:MarkupsModule|Markups Module]] (Nicole Aucoin)
* [[2014_Winter_Project_Week:Logging|Logging (standardization, logging to file)]] (Nicole Aucoin, Steve Pieper, Jc, Andras Lasso, Csaba Pinter, ???)
*[[2014_Project_Week:CLI|CLI]] (Jim Miller)
* [[2014_Winter_Project_Week:Steered Registration|Steered Registration (LandmarkRegistration module)]] (Steve, Greg, Kevin, Vinicius, Marcel)
* [[2014_Winter_Project_Week:MRB Extension Dependencies|MRB Extension Dependencies]] (Steve, Jc, Jim, Nicole, Alex)
* [[2014_Winter_Project_Week:SubjectHierarchy|Subject hierarchy]] (Csaba Pinter, Andras Lasso, Steve Pieper, Jc, Jayashree, John, Alireza, Andrey)
* [[2014_Winter_Project_Week:IntegrationOfContourObject|Integration of Contour object]] (Csaba Pinter, Andras Lasso, Steve Pieper, ???)
* [[2014_Winter_Project_Week:NonlinearTransforms|Integration nonlinear transforms]] (Alex Yarmarkovich, Csaba Pinter, Andras Lasso, Steve Pieper, ???)
* [[2014_Winter_Project_Week:ParameterSerialization | JSON Parameter Serialization]] (Matt McCormick, Steve Pieper, Jim Miller)
* [[2014_Winter_Project_Week:XNATSlicerLink| 3DSlicer annotations in XNAT]] (Erwin Vast, Nicole Aucoin, Andrey Fedorov)
* [[2014_Winter_Project_Week:PlanarImage|Planar Images]] (Franklin King, Csaba Pinter, Andras Lasso)

2014 Winter Project Week

2014-01-06T16:54:24Z

Hjmjohnson: /* Huntington's Disease */

Back to [[Project Events]], [[AHM_2014]], [[Events]]

__NOTOC__
[[image:PW-SLC2014.png|300px]]

Project Week is a hands on activity -- programming using the open source [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the NA-MIC, NCIGT, and NAC calendars. It is held in the summer at MIT, typically the last week of June, and a shorter version is held in Salt Lake City in the winter, typically the second week of January.

Active preparation begins 6-8 weeks prior to the meeting, when a kick-off teleconference is hosted by the NA-MIC Engineering, Dissemination, and Leadership teams, the primary hosts of this event. Invitations to this call are sent to all NA-MIC members, past attendees of the event, as well as any parties who have expressed an interest in working with NA-MIC. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient NA-MIC coverage for all. Subsequent teleconferences allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams are asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself starts off with a short presentation by each project team, driven using their previously created description, and allows all participants to be acquainted with others who are doing similar work. In the rest of the week, about half the time is spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half is spent in project teams, doing hands-on programming, algorithm design, or clinical application of NA-MIC kit tools. The hands-on activities are done in 10-20 small teams of size 3-5, each with a mix of experts in NA-MIC kit software, algorithms, and clinical. To facilitate this work, a large room is setup with several tables, with internet and power access, and each team gathers on a table with their individual laptops, connects to the internet to download their software and data, and is able to work on their projects. On the last day of the event, a closing presentation session is held in which each project team presents a summary of what they accomplished during the week.

A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].
= Dates.Venue.Registration =

Please [[AHM_2014#Dates_Venue_Registration|click here for Dates, Venue, and Registration]] for this event.

= [[AHM_2014#Agenda|'''AGENDA''']] and Project List=

Please:
* [[AHM_2014#Agenda|'''Click here for the agenda for AHM 2014 and Project Week''']].
* [[#Projects|'''Click here to jump to Project list''']]

=Background and Preparation=

A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].

Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]

=Projects=
* [[2014_Project_Week_Template | Template for project pages]]

==TBI==
*[[2014_Project_Week:TBIatrophy|Multimodal neuroimaging for the quantification of brain atrophy at six months following severe traumatic brain injury]] (Andrei Irimia, SY Matthew Goh, Carinna M. Torgerson, John D. Van Horn)
*[[2014_Project_Week:TBIdemyelination|Systematic evaluation of axonal demyelination subsequent to traumatic brain injury using structural T1- and T2-weighted magnetic resonance imaging]] (Andrei Irimia, SY Matthew Goh, Carinna M. Torgerson, John D. Van Horn)
*[[2014_Project_Week:BrainAging|Mapping the effect of traumatic brain injury upon white matter connections in the human brain using 3D Slicer]] (Andrei Irimia, John D. Van Horn)
*[[2014_Project_Week:LongitudinalDTI|Patient-specific longitudinal DTI analysis in traumatic brain injury]] (Anuja Sharma, Andrei Irimia, Bo Wang, John D. Van Horn, Martin Styner, Guido gerig)
*[[2014_Project_Week:TBISegmentation|Testing the interactive segmentation algorithm for traumatic brain injury]] (Bo Wang, Marcel Prastawa, Andrei Irimia, John D. Van Horn, Guido Gerig)

==Atrial Fibrillation==
*[[2014_Project_Week:MRAFusionRegistration|DEMRI LA Segmentation via Image Fusion (MRA)]] (Josh, Salma, Alan)
*[[2014_Project_Week:LAFibrosisVisualizationModule|LA Fibrosis / Scar Visualization]] (Josh, Salma, Alan)
*[[2014_Project_Week:CARMADocumentation|CARMA Extension Documentation Project]] (Josh, Salma)
*[[2014_Project_Week:GraphCutsLASegmentationModule|LA Segmentation module using multi-column Graph Cuts]] (Gopal, Salma, Josh, Rob, Ross)
*[[2014_Project_Week:JointImageAndShapeAnalysisForFibrosisDistribution|Joint Image and Shape Analysis for Fibrosis Distribution]](Yi Gao, LiangJia Zhu, Josh Cates, Rob MacLeod, Sylvain Bouix, Ron Kikinis, Allen Tannenbaum)
*[[2014_Project_Week:GrowCutLevelSetLA|Grow cut, level set integration for interactive LA segmentation]] ( Liangjia Zhu, Ivan Kolesov, Yi Gao, Allen Tannenbaum)

==Huntington's Disease==
*[[2014_Project_Week:DWIDispersion|DWI Dispersion]] (Hans, CF, Peter Savadjiev)
*[[2014_Project_Week:Modules scripting|Slicer module scripting?]] (Dave)
*[[2014_Project_Week:DWIConverter|DWIConverter?]] (Hans, Kent)
*[[2014_Project_Week:Slicer_Based_Surface_Template_Estimation|Slicer Based Surface Template Estimation]] (Saurabh Jain, Steve Pieper, Hans Johnson, Josh Cates)
*[[2014_Project_Week:HD_4DShapes|4D shape analysis: application to HD ]] (James Fishbaugh,Hans Johnson, Guido Gerig)
*[[2014_Project_Week:Shape_Registration_and_Regression|Shape registration and regression in Slicer4 ]] (James Fishbaugh,Hans Johnson, Guido Gerig)

==Head and Neck Cancer==
*[[2014_Project_Week:DIR_validation|DIR Validation]] (Nadya and Greg)
*[[2014_Project_Week:Hybrid_bspline|Hybrid B Spline]] (Nadya, Greg, Steve)
*[[2014_Project_Week:CarreraSlice|Interactive Segmentation]] (Ivan, LiangJia, Nadya, Yi, Greg, Allen)

==Slicer4 Extensions==
*[[2014_Project_Week:ShapePopulationViewer|Surface Visualization - ShapePopulationViewer]] (Alexis Girault, Francois Budin, Beatriz Panaigua, Martin Styner)
*[[2014_Project_Week:DTIAnalysisPipeline|DTI Analysis Pipeline as Slicer4 Extensions]] (Francois Budin, Martin Styner)

==Cardiac==
*[[2014_Project_Week:CardiacStemCellMonitoring|Monitoring engrafted stem cells in cardiac tissue with time series manganese enhanced MRI]] (Karl Diedrich)
*[[2014_Project_Week:CardiacCongenitalSegmentation|Whole-heart segmentation of cardiac MR images in congenital heart defect cases]] (Danielle Pace, Polina Golland)

==Stroke==

*[[2014_Project_Week:Multi-Tissue_Stroke_Segmentation|Multi-Tissue Stroke Segmentation]] (Ramesh, Polina B., Polina G.)

==Brain Segmentation==
*[[2014_Project_Week:MultiAtlas_MultiImage_Segmentation|Multi-Atlas based Multi-Image Segmentation]] (Minjeong Kim, Xiaofeng Liu, Jim Miller, Dinggang Shen)

==Image-Guided Interventions==
*[[2014_Project_Week:OpenIGTLink| OpenIGTLink Interface: New data types and structures]] (Junichi Tokuda, Andras Lasso, Steve Piper, ???)
*[[2014_Project_Week:Ultrasound Visualization and Navigation in Neurosurgery|Ultrasound Visualization and Navigation in Neurosurgery]] (Matthew Toews, Alireza Mehrtash, Csaba Pinter, Andras Lasso, Steve Pieper, William M. Wells III)
*[[2014_Project_Week:PercutaneousApproachAnalysis| Percutaneous Approach Analysis]] (Atsushi Yamada, Junichi Tokuda, Koichiro Murakami, ??)
*[[2014_Project_Week:EndoscopeConsole| Endoscope Console]] (Atsushi Yamada, Junichi Tokuda, ??)
*[[2014_Project_Week:Statistical Shape Model for robotic spine surgery| Statistical Shape Model for robotic spine surgery]] (Marine Clogenson, ???)
*[[2014_Project_Week:ImmersiveVR| Immersive VR devices]] (Franklin King, Andras Lasso)

==Radiation Therapy==
*[[2014_Project_Week:DICOM_RT|DICOM RT Export]] (Greg Sharp, Kevin Wang, others??)
*[[2014_Project_Week:DICOM_SRO|DICOM Spatial Registration Export]] (Greg Sharp, Kevin Wang, others??)
*[[2014_Project_Week:Registration_Evaluation|Interactive Registration and Evaluation]] (Kevin Wang, Steve Pieper, Greg Sharp)
*[[2014_Project_Week:External_Beam_Planning|External Beam Planning Visualization]] (Kevin Wang, Greg Sharp, Csaba Pinter)

==TMJ-OA==
* [[2014_Winter_Project_Week:Constrain Fiducial along Suface|Constrain Fiducial along Suface]] (Vinicius Boen, Nicole Aucoin, Beatriz Paniagua)
* [[2014_Winter_Project_Week:Cropping Multiple Surfaces|Cropping multiple surfaces simultaneously]] (Alexander, Jc, Steve, Vinicius, Beatriz Paniagua)
* [[2014_Winter_Project_Week:Color Code Tables|Color Coded Tables]] (Vinicius Boen, Beatriz Paniagua, Nicole Aucoin, Steve Pieper, Francois Budin)
* [[2014_Winter_Project_Week:4DShape Analysis of mandibular changes|4DShape Analysis of mandibular changes]] (Vinicius Boen, James Fishbaugh, Guido Gerig)

==Chronic Obstructive Pulmonary Disease ==
* [[2014_Winter_Project_Week:CIP Core|Chest Imaging Platform (CIP) - Core Infrastructure]] (Raul San Jose, Rola Harmouche, Pietro Nardelli, James Ross)
* [[2014_Winter_Project_Week:CIP Infrastructure Testing and SuperBuild|CIP Testing and SuperBuild]] (James Ross, Raul San Jose)
* [[2014_Winter_Project_Week:Slicer CIP Slicer MRML| Slicer CIP- MRML consolidation]] (Pietro Nardelli, Rola Harmouche, James Ross, Raul San Jose)
* [[2014_Winter_Project_Week:Slicer CIP Modules| Slicer CIP- Modules]] (Rola Harmouche, Pietro Nardelli, James Ross, Raul San Jose)

==[http://qiicr.org QIICR]==

*[[2014_Project_Week:4D_NIfTI_Multivolume|4D NIfTI Multivolume Support]] (Jayashree, Andrey, Jim, John)
*[[2014_Project_Week:RT_FormatConversions|RT and ITK Format Conversions]] (Jayashree, Andras, Csaba. John)
*[[2014_Project_Week:BatchConvertDICOM|Python Scripting Slicer DICOM read/write to convert segmentation objects]] (Jayashree, Andrey, Alireza, Steve, Jc, Hans, John)
*[[2014_Project_Week:PkModeling_user_tool|User module for DCE modeling]] (Andrey, Jayashree, Jim, Alireza, Steve, Ron)
*[[2014_Project_Week:DICOM_enhanced_multiframe|DICOM enhanced multiframe object support]] (Andrey, Alireza, David Clunie, Jayashree, Steve, Reinhard, Jim)
*[[2014_Project_Week:Quantitative_Index_Computation|Quantitative Index Computation]] (Ethan Ulrich, Reinhard Beichel, Nicole, Andrey, Jim)
*[[2014_Project_Week:TCIA Browser Extension in Slicer|TCIA Browser Extension in Slicer]] (Alireza, Andrey, Steve, Ron)

==Infrastructure==
*[[2014_Project_Week:MRMLSceneSpeedUp|MRML Scene speed up]] (Jc, Andras Lasso)
*[[2014_Project_Week:MultidimensionalDataSupport|Multidimensional data support]] (Andras Lasso, Andriy Fedorov, Steve Pieper, JC, Kevin Wang)
*[[2014_Project_Week:MarkupsModule|Markups Module]] (Nicole Aucoin)
* [[2014_Winter_Project_Week:Logging|Logging (standardization, logging to file)]] (Nicole Aucoin, Steve Pieper, Jc, Andras Lasso, Csaba Pinter, ???)
*[[2014_Project_Week:CLI|CLI]] (Jim Miller)
* [[2014_Winter_Project_Week:Steered Registration|Steered Registration (LandmarkRegistration module)]] (Steve, Greg, Kevin, Vinicius, Marcel)
* [[2014_Winter_Project_Week:MRB Extension Dependencies|MRB Extension Dependencies]] (Steve, Jc, Jim, Nicole, Alex)
* [[2014_Winter_Project_Week:SubjectHierarchy|Subject hierarchy]] (Csaba Pinter, Andras Lasso, Steve Pieper, Jc, Jayashree, John, Alireza, Andrey)
* [[2014_Winter_Project_Week:IntegrationOfContourObject|Integration of Contour object]] (Csaba Pinter, Andras Lasso, Steve Pieper, ???)
* [[2014_Winter_Project_Week:NonlinearTransforms|Integration nonlinear transforms]] (Alex Yarmarkovich, Csaba Pinter, Andras Lasso, Steve Pieper, ???)
* [[2014_Winter_Project_Week:ParameterSerialization | JSON Parameter Serialization]] (Matt McCormick, Steve Pieper, Jim Miller)
* [[2014_Winter_Project_Week:XNATSlicerLink| 3DSlicer annotations in XNAT]] (Erwin Vast, Nicole Aucoin, Andrey Fedorov)
* [[2014_Winter_Project_Week:PlanarImage|Planar Images]] (Franklin King, Csaba Pinter, Andras Lasso)

2014 Project Week:DWIDispersion

2014-01-06T16:53:41Z

Hjmjohnson: /* Key Investigators */

==Key Investigators==
* Iowa: Hans Johnson
* Iowa: Kent Williams
* BWH: C-F Westin
* BWH: Peter Savadjiev

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
Implement the fiber dispersion computation method of Savadjiev et al. (MICCAI 2012) as a Slicer4 Extension. Convert the currently existing Matlab implementation into C++/ITK and test it on various datasets.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Create a realistic test suite based on Huntington datasets for the Matlab code.
** [HANS - Monday] Prepare test DWI data set for preparing data

* Create a VTK reader/writer in matlab, in order to the test the matlab code.
** [KENT -- DONE] git@github.com:BRAINSia/CompressedSensingDWI.git
** [PETER - Monday] Build github version of readers/writers
** [PETER - Monday] Manually test vtk readers/writers, and convert existing test to use the binary forms

* Convert the Matlab code to C++/ITK
** [HANS/PETER - Monday/Tuesday] Create design document (i.e. this page and paer/pencil) to describe the intended inputs and outputs.
** [PETER -- Monday] - Write desired command line interface psuedocode "caluclateDispersion --inputTract <wholebrain.vtp> --mask <roi.nrrd> --outputTract <decoratedversionofinput.vtp> "
** [HANS/PETER -- Monday] - Create shell program in psydocode/comments with XML and cxx files with description of basic IO programming needed
** [KENT -- Tuesday/Wednesday] -- Fill in I/O portions of psuedocode and make a compilable application that reads the inputTract, breaks it apart into necessary algorithmic components, and writes out the outputTract.

*Create a Slicer extension

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Private git repository created at: git@github.com:BRAINSia/CompressedSensingDWI.git

</div>
</div>

2014 Project Week:DWIDispersion

2014-01-06T16:53:11Z

Hjmjohnson: /* Project Description */

==Key Investigators==
* Iowa: Hans Johnson
* BWH: C-F Westin
* BWH: Peter Savadjiev

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
Implement the fiber dispersion computation method of Savadjiev et al. (MICCAI 2012) as a Slicer4 Extension. Convert the currently existing Matlab implementation into C++/ITK and test it on various datasets.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Create a realistic test suite based on Huntington datasets for the Matlab code.
** [HANS - Monday] Prepare test DWI data set for preparing data

* Create a VTK reader/writer in matlab, in order to the test the matlab code.
** [KENT -- DONE] git@github.com:BRAINSia/CompressedSensingDWI.git
** [PETER - Monday] Build github version of readers/writers
** [PETER - Monday] Manually test vtk readers/writers, and convert existing test to use the binary forms

* Convert the Matlab code to C++/ITK
** [HANS/PETER - Monday/Tuesday] Create design document (i.e. this page and paer/pencil) to describe the intended inputs and outputs.
** [PETER -- Monday] - Write desired command line interface psuedocode "caluclateDispersion --inputTract <wholebrain.vtp> --mask <roi.nrrd> --outputTract <decoratedversionofinput.vtp> "
** [HANS/PETER -- Monday] - Create shell program in psydocode/comments with XML and cxx files with description of basic IO programming needed
** [KENT -- Tuesday/Wednesday] -- Fill in I/O portions of psuedocode and make a compilable application that reads the inputTract, breaks it apart into necessary algorithmic components, and writes out the outputTract.

*Create a Slicer extension

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Private git repository created at: git@github.com:BRAINSia/CompressedSensingDWI.git

</div>
</div>

DBP Iowa Huntington's Disease 2014

2013-12-12T20:36:49Z

Hjmjohnson:

[[AHM_2014#Agenda|Back to AHM_2014 Agenda]]
*Time 4-5pm
*Goal: Final polishing of developed tools for application to large multi-site DWI data.
**Review tools from the git@github.com:BRAINSia/NAMICExternalProjects.git and ensure that complete set of necesasry tools exist
#External_ANTs.cmake
#External_BRAINSTools.cmake
#External_Cppcheck.cmake
#External_DCMTK.cmake
#External_DTIPrep.cmake
#External_DTIProcess.cmake
#External_DTIReg.cmake
#External_DTI_Tract_Stat.cmake
#External_Eigen.cmake
#External_ITKv4.cmake
#External_MultiAtlas.cmake
#External_NIPYPE.cmake
#External_SimpleITK.cmake
#External_SlicerExecutionModel.cmake
#External_SlicerJointRicianAnisotropicLMMSEFilter.cmake
#External_UKF.cmake
#External_UnbiasedNonLocalMeans.cmake
#External_VTK.cmake
#External_teem.cmake
#External_tract_querier.cmake
#External_zlib.cmake

**Modify the existing Slicer modules so that they are stream-lined and can comunicate better together
**Discuss which of the internal modules should be re-bundled into a cohesive package
**Create Slicer workflows (SimpleITK+Python+NIPYPE provides this in the non-stable releases) We need JC to help with this.

*DBP PI: Hans Johnson
*Algorithms as CLI modules: Martin Styner, Francois Budin, UNC
# Work need so done to make tools more work better together. In particular, masking operations need implicit resampling to be included. Currently if the spaces for the mask and the images are even 1e-6 off, then the programs will refuse to run.

*Engineering: workflows in collaboration with DBP: Dan Marcus
# Extensions to XNAT to support **MASSIVE** amounts of derived data integration.

2013 Summer Project Week:SinglePrecisionRegistrationITK

2013-06-21T12:17:47Z

Hjmjohnson:

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
</gallery>

[[Image:GreenDashboardForSinglePrecision.png|900px]]

==Key Investigators==
* UIowa: Ali Ghayoor, Hans, Dave
* NLM: Brad Lowekamp

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>

The current registration framework of ITK just can process data using double precision. However, in some cases using 'float' type is enough for the precision of computations.

This feature allows CPU to process more data in its cache in a limited period of time, so it can increase the computations speed. Also, writing outputs to the disk using single precision needs much less memory rather than we save them by values in double precision.
Saving the memory space is specially important when our outputs are huge files that need hundreds of giga bytes of memory disk. An example of such outputs is transforms files that contain several deformation fields.

To make ANTS capable to do its computations in single point precision, first, we need improve ITK for this purpose.
Currently registration framework of ITK, just can use 'double' precision for its internal computations, so we should add single precision (float Type) as another possible option.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>

This project will be considered successfully executed when the following deliverables are accepted:

1- A new flag is added to antsRegistration to run it on single precision mode. For now, it can be called "--float".

2- A template parameters of "T", that defines the precision type, is added to all classes needed by antsRegistration if it cannot be extracted inside the class.

3- Currently ITK cannot be used in single precision. Necessary changes should be taken to make ITK be able to do its processing in single precision. (It is defined as a Sub-Task to this ticket).

4- Make sure that the ITK-Standalone is built based on new changes.

5- Build ANTS using the new local version of ITK when float mode is on.

6- Fix all possible compiler errors in ANTS codes or ITK new version codes when ANTS is compiling using the new ITK, and the float mode is on.

7- We can make sure that the ANTS and ITK are now compatible with single precision mode if the build process is done successfully (all compiler and linker errors are fixed).

8- Design a simple experiment to catch the running time errors (you may need to use GDB).

9- If antsRegistration can be run successfully, it is time to start evaluation steps. Evaluate the efficiency of new feature using the following criteria:
I) Compare the running time of antsRegistration on the float mode with the case that it is run on double precision mode. Experiments should be run on the same system.
II) Compare the precision of registration task between the single and double precision modes. We can run antsRegistration using the "print-similarity-measure-interval" flag that prints out the CC similarity metric measure on iterations intervals.

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
# ITK is built successfully, and all test pass, and no compiler warnings on Windows, Mac, Linux. [http://review.source.kitware.com/#/c/11396/ Gerrit Review process] (BIG THANKS TO BRAD LOWEKAMP!)
# ANTS tool build against this version successfully,
# BRAINSTools built agains this successfully,
# Slicer Built against this successfully
# Small regression in SimpleITK resolved with small patch to SimpleITK [http://review.source.kitware.com/#/c/11696/ Gerrit Fix for SimpleITK]
The last patch is sent to gerrit and it is under review.
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as an improvement to the underlying ITK library. It provides opportutinity for CLI modules to take advantage of single precision registration and transformations where appropriate to provide potential significant speed increases. At least 1 test case showed 30% speed improvement.

File:GreenDashboardForSinglePrecision.png

2013-06-21T12:07:47Z

Hjmjohnson: Shows green dashboard for Single precision.

Shows green dashboard for Single precision.

2013 Summer Project Week:Investigate Potential Tensor Computation Improvement via Positive Semi-Definite (PSD) Tensor Estimation

2013-06-21T11:58:00Z

Hjmjohnson: /* Background */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:PSD_NewOption.png|How the CLI needs to expose a new feature for PSD.
</gallery>

==Key Investigators==
* BWH: Raul San Jose, Carl-Fredrik Westin, Demian Wassermann
* UNC: Marc Niethammer
* UIowa: Hans Johnson, Joy Matsui

==Background==
Tensor estimation in Slicer4 is done by vtkTeemEstimateDiffusionTensor. In the inner loop of this class, the tensor fitting is actually computed by _tenEstimate1TensorSingle (teem/src/ten/estimate.c). The solution that teem takes to deal with negative eigenvalues is to add an isotropic part corresponding to the smallest eigenvalue if the eigenvalue is negative and the flag negEvalShift is On. This flag is part of the tenContext structure that controls the estimation options and, in turn, can be set in the vtk class by means of ShiftNegativeEigenvalues. By default, ShiftNegativeEigenvalues is Off in the constructor.

Long story short, teems shifts the value of the eigenvalues so the most negative eigenvalue becomes zero that it is not what it is exactly done in the PSD constrained paper. I've (Raul) been digging through the old slicer2 repository but I did not find that implementation. I'm sure that we played with it but it never made it to any of the CSV branches !!! (old stuff, as you can see). I recalled that we used to do the correction when computing the scalar quantities rather than at tensor estimation. But, surprise, surprise, I found the code in Slicer4. It is funny how you forget things that you have done. I believe this code has traveled through the time machine of Slicer2, to Slicer3 and now to Slicer4.

If you check vtkDiffusionTensorMathematics you will find the magic in FixNegativeEigenvaluesMethod
[https://github.com/Slicer/Slicer/blob/master/Libs/vtkTeem/vtkDiffusionTensorMathematics.cxx#L922]

However, if you go to the ExecuteData, this method is commented in favor of applying the same approach that teem applies. I'm sure that this was, at the time, an unconscious decision to be consistent.

I have to say that this might be a good time to revisit this issue and add some consistency across the code about where to apply this kind of tricks. The PSD trick is only valid under the least-square solution, so it would be the most sense to apply it as an option in vtkTeemEstimationDiffusionTensor when the LS method is selected. I don't know if this can be generalized to the WLS but my experience is that WLS deals with many of this negative eigenvalues oddities when it weights down the noise DWIs.

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>

Discuss approach and schedule making this change after project week.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>

# Modify the CLI code to expose the alternate analysis processing schemes at runtime rather than at compile time
# Modify XML to expose option in the Slicer GUI

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>

Discussions occured, and it was determined that this work is best done after project week.

[[File:DWItoDTI_with_PSD_EmailConversation.pdf]] E-mail conversation

</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as an improvement to the existing DWItoDTI module

==References==
* [http://lmi.bwh.harvard.edu/papers/pdfs/2006/niethammerEMBS06.pdf On Diffusion Tensor Estimation]

2013 Summer Project Week:Investigate Potential Tensor Computation Improvement via Positive Semi-Definite (PSD) Tensor Estimation

2013-06-21T11:56:25Z

Hjmjohnson:

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:PSD_NewOption.png|How the CLI needs to expose a new feature for PSD.
</gallery>

==Key Investigators==
* BWH: Raul San Jose, Carl-Fredrik Westin, Demian Wassermann
* UNC: Marc Niethammer
* UIowa: Hans Johnson, Joy Matsui

==Background==
Tensor estimation in Slicer4 is done by vtkTeemEstimateDiffusionTensor. In the inner loop of this class, the tensor fitting is actually computed by _tenEstimate1TensorSingle (teem/src/ten/estimate.c). The solution that teem takes to deal with negative eigenvalues is to add an isotropic part corresponding to the smallest eigenvalue if the eigenvalue is negative and the flag negEvalShift is On. This flag is part of the tenContext structure that controls the estimation options and, in turn, can be set in the vtk class by means of ShiftNegativeEigenvalues. By default, ShiftNegativeEigenvalues is Off in the constructor.

Long story short, teems shifts the value of the eigenvalues so the most negative eigenvalue becomes zero that it is not what it is exactly done in the PSD constrained paper. I've (Raul) been digging through the old slicer2 repository but I did not find that implementation. I'm sure that we played with it but it never made it to any of the CSV branches !!! (old stuff, as you can see). I recalled that we used to do the correction when computing the scalar quantities rather than at tensor estimation. But, surprise, surprise, I found the code in Slicer4. It is funny how you forget things that you have done. I believe this code has traveled through the time machine of Slicer2, to Slicer3 and now to Slicer4.

If you check vtkDiffusionTensorMathematics you will find the magic in FixNegativeEigenvaluesMethod
[https://github.com/Slicer/Slicer/blob/master/Libs/vtkTeem/vtkDiffusionTensorMathematics.cxx#L922]

However, if you go to the ExecuteData, this method is commented in favor of applying the same approach that teem applies. I'm sure that this was, at the time, an unconscious decision to be consistent.

I have to say that this might be a good time to revisit this issue and add some consistency across the code about where to apply this kind of tricks. The PSD trick is only valid under the least-square solution, so it would be the most sense to apply it as an option in vtkTeemEstimationDiffusionTensor when the LS method is selected. I don't know if this can be generalized to the WLS but my experience is that WLS deals with many of this negative eigenvalues oddities when it weights down the noise DWIs.

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>

Discuss approach and schedule making this change after project week.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>

# Modify the CLI code to expose the alternate analysis processing schemes at runtime rather than at compile time
# Modify XML to expose option in the Slicer GUI

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>

Discussions occured, and it was determined that this work is best done after project week.

[[DWItoDTI_with_PSD_EmailConversation.pdf]] E-mail conversation

</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as an improvement to the existing DWItoDTI module

==References==
* [http://lmi.bwh.harvard.edu/papers/pdfs/2006/niethammerEMBS06.pdf On Diffusion Tensor Estimation]

File:PSD NewOption.png

2013-06-21T11:50:10Z

Hjmjohnson: A picture of where in slicer an update to the DWItoDTI processing needs another option.

A picture of where in slicer an update to the DWItoDTI processing needs another option.

File:DWItoDTI with PSD EmailConversation.pdf

2013-06-21T11:49:26Z

Hjmjohnson: An e-mail conversation about fixing Slicer.

An e-mail conversation about fixing Slicer.

Learn and Apply FiberBundleLabelSelect for Huntington's Disease Data

2013-06-21T11:37:46Z

Hjmjohnson: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* UIowa: Hans Johnson
* BWH: Demian Wasserman

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
Integrate processing Freesurfer, BRAINSTools, and Slicer's FiberBundleLabelSelect

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>

1) Label based tractography modules

2) Auto run paint updates training

3) Request "dictionary" of regional include/excludes

4) Need filter bundle as input

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
After Discussion with Demian, we determined that the the tract querier ([http://www.na-mic.org/Wiki/index.php/2013_Summer_Project_Week:WMQL_Integration_in_Slicer See WMQL project page ] and [ http://ww4.aievolution.com/hbm1201/index.cfm?do=abs.viewAbs&abs=6409 Poster ] ) was a better fit for the HD processing needs.

</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline
##Extension -- loadable
#Other (Please specify)

==References==
'''TODO'''

Learn and Apply FiberBundleLabelSelect for Huntington's Disease Data

2013-06-17T17:12:52Z

Hjmjohnson: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* UIowa: Hans Johnson
* BWH: Demian Wasserman

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
Integrate processing Freesurfer, BRAINSTools, and Slicer's FiberBundleLabelSelect

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>

1) Label based tractography modules

2) Auto run paint updates training

3) Request "dictionary" of regional include/excludes

4) Need filter bundle as input

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>

</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline
##Extension -- loadable
#Other (Please specify)

==References==
'''TODO'''

2013 Project Week Breakout Session: SimpleITK

2013-06-13T20:27:30Z

Hjmjohnson:

[[2013_Summer_Project_Week#Agenda|Back to Summer project week Agenda]]

Presenters: Hans Johnson & Bradley Lowekamp

== Background ==

SimpleITK is an abstraction layer on top of ITK which provides Python bindings for many of the algorithms in ITK. The tool is under active development and recent additions have focus on providing a more Pythonic interface to the Image class, numerous additional algorithms, along with the addition of transforms and interpolators.

SimpleITK is currently a build option in Slicer3D when using ITKv4. It can provide access to many powerful algorithms in Slicer as python modules or SimpleITK can be used in the Python Interactor for image manipulation and segmentation.

Version 0.6.1 is currently available as a binary download, and is also being incorporated into Slicer.

== Summary ==

This session will consists of interactive demonstrations of the fundamental concepts and style of SimpleITK along with showing the latest features in the 0.6 release. The presentation will make use of matplotlib and the Scientific Python environment to illustrate a Pythonic workflow to perform common image tasks and segmentation.

== Attendee Preparation ==

You can set up your own environment or you can use a server that has been set up for the group in the conference room.

=== Setting up your Own Environment ===

Follow the instructions below to set up your own environment.

Attendees are encouraged to setup a python environment to follow along during this session.

Under the best of circumstances (tested on OSX 10.8 and 10.7.5) this environment can be setup with the following:

sudo pip install virtualenv
virtualenv ~/sitkpy --no-site-packages
~/sitkpy/bin/pip install ipython
~/sitkpy/bin/pip install ipython[zmq]
~/sitkpy/bin/pip install tornado
~/sitkpy/bin/pip install numpy
~/sitkpy/bin/pip install matplotlib

===Install SimpleITK 0.6.1 ===

Download the built egg for your system from Source Forge:
http://sourceforge.net/projects/simpleitk/files/SimpleITK/0.6.1/Python/

Use easy_install to install or upgrade:

~/sitkpy/bin/easy_install -U SimpleITK-0.6.1_gc9d89-py$(python version)-$(OS)-$(arch).egg

If there is not a built distribution for your system you will need to build SimpleITK:
http://www.itk.org/Wiki/ITK_Release_4/SimpleITK/GettingStarted#Build_It_Yourself

===Download the course material===

The "notebooks" are available for download as a git repository:

git clone git@github.com:SimpleITK/SimpleITK-Notebooks.git

Additionally the SPL's "Multi-modality MRI-based Atlas of the Brain" should be downloaded and extracted into the SimpleITK-Notebooks/Data directory.

http://www.spl.harvard.edu/publications/item/view/2037

===Run the environment===

To launch:
cd SimpleITK-Notebooks
~/sitkpy/bin/ipython notebook --pylab=inline

Note: On Linux platforms you may be able to obtain many of these packages as system packages which may suffice ( Ubuntu 12+).
Note: On Window platforms some of these packages should be obtained as binary downloads and installed.

File:20130110 IowaDBPProgress.pdf

2013-01-10T19:12:34Z

Hjmjohnson: 2013 Progress Report

2013 Progress Report

2012 Summer Project Week:ITKv4 Integration

2012-06-22T13:49:52Z

Hjmjohnson: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:ITKv4Integration-screenshot.png| Screenshot
</gallery>

==Key Investigators==
* Iowa: Hans Johnson, Kent Williams
* GE: Jim Miller
* SPL: Steve Pieper
* Kitware: JC, Julien
* NLM (C): Bradley Lowekamp
* NoWare: Bill Lorensen

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
# Move Slicer build from ITKv3 to ITKv4
## Complete build from scratch with packaging
## Build against ITKv4
## Build with SimpleITK
# Pass Rule 1 and Rule 2 of "Rons Rules for tools"
## You make it, I break it. [1]
## Your tool does not exist, until it works on my laptop with my data. [2]

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
Figure out how to get packaging working when building with ITKv4
* Basic building is working (Has been for a long time).
* Compiler propagation to submodules needed

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
*
During Project Week we resolved the packaging issues.
# ITKv4 now supports runtime only installs. (Thanks Bill Lorensen)
## This required changes to both Slicer and ITKv4 (for complete compliance).
### The Slicer changes are checked into the repo.
### The ITKv4 changes are tested and merged into master branch of ITKv4
### BRAINSTools was cleaned up to support the COMPONENT Runtime Install

# Clean build process
## Remove configuration warnings about unnecessary/unused configuration commands
## Fix shared library linking for python on Mac for creating successful install
## Complete build success tested to respect superbuild requested compiler (set default CC=/dev/null and CXX=/dev/null to force errors)
##
</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

As part of the CMake build system

==References==

http://www.na-mic.org/Bug/view.php?id=2007

</div>

2012 Summer Project Week:DicomToNrrd

2012-06-21T20:59:18Z

Hjmjohnson: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Iowa: Kent Williams, Hans Johnson

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
Revise and refactor the DicomToNrrd program to build properly with ITK 4.1. Enhance it to accept a wider variety of DICOM Diffusion Weighted Images.

The program needs to be compliant with DCMTK version that will be in future Slicer versions.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
Starting from the original DIcomToNrrd program (as it exists in the Slicer3/Slicer4 source code),
modify the program to satisfy the following goals:

Make it compatible with ITK 4. The old version made direct calls to GDCM version 1 APIs, and ITK 4 incorporates GDCM 2, which is not compatible.

Re-write the existing code to be more readable and maintainable.

Add more regression tests, incorporating new test images that were not readable with the old version of DicomToNRRD.

Prepare for DCMTK integration by using system version of DCMTK

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
Intial goals for this project are complete.
* The program successfully reads all test images as the earlier ITK3-only version of DicomToNrrd.
* It can also handle several image 'flavors' that caused the earlier version to fail.
* Test images contributed by the Slicer community have been added to the testing data corpus, which is stored on MIDAS (http://midas.kitware.com)

New goals have made progress, but have not been finalized
* ITK integration with new DCMTK is located at: http://review.source.kitware.com/#/c/5989/12
* http://git.dcmtk.org/dcmtk.git.rt tag "f2b71c92461085718f3bccd1c7415382d3e11e3a"
* Verified that DICOM-RT version of DCMTK builds without obvious errors.

</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module - NO
#Slicer Module
##Built-in - NO
##Extension -- commandline - YES
##Extension -- loadable - NO
#Other

==References==

2012 Summer Project Week

2012-06-21T20:48:19Z

Hjmjohnson: /* Huntington's Disease */

Back to [[Events]]

[[image:PW-MIT2012.png|200px]]

*'''Dates:''' June 18-22, 2012
*'''Location:''' MIT

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 18
!style="width:18%" |Tuesday, June 19
!style="width:18%" |Wednesday, June 20
!style="width:18%" |Thursday, June 21
!style="width:18%" |Friday, June 22
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''9am-10am:''' [[2012 Project Week Breakout Session: Slicer4|What's new in Slicer4 (Charts - Jim, DICOM - Steve, Multivolume - Andrey)]] <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
<br>----------------------------------------<br>
'''10-11am''' [[2012 Project Week Breakout Session:Slicer4 Python Q&A|Slicer4 Python Q&A]] <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
|'''9am-11pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2012 Project Week Breakout Session: SimpleITK|Slicer and SimpleITK]] (Hans)
[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
<br>----------------------------------------<br>
'''10am-12pm: <font color="#4020ff">Computation Core PIs: closed meeting with Ron:'''</font><br>
[[MIT_Project_Week_Rooms#Star|Star Room]]
|'''9am-12pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2012 Summer Project Week Breakout Session:Slicer in Networked Environment|Slicer in Networked Environment]] (Junichi)
[[MIT_Project_Week_Rooms#Kiva_32-G449|Grier Room]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-4:30pm''' [[2012 Summer Project Week Breakout Session:SlicerExtensions|Slicer4 Extensions]] (JC) <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]
|'''3-4pm:''' [[2012_Tutorial_Contest|Tutorial Contest Presentations]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''4-5pm:''' [[2012 Summer Project Week Breakout Session:Slicer DICOM|Breakout Session: DICOM, Networking, RT, Segmentations]] (Steve, Greg, Andras, Andre)
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''12:45-1pm:''' [[Events:TutorialContestJune2012|Tutorial Contest Winner Announcement]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3-30pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2012 Summer Project Week Breakout Session:QtTesting|QtTesting]] (JC)
|'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2012 Summer Project Week Breakout Session:Ultrasound|Ultrasound]] (Tamas)
[[MIT_Project_Week_Rooms#Kiva_32-G449|Grier Room]]
<br>----------------------------------------<br>
'''3:00-4:00pm''' [[2012_Summer_Project_Week:LeanSlicer|Lean Slicer (Andras)]]<br>
[[MIT_Project_Week_Rooms#Kiva_32-G449|Grier Room]]
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

==Projects==

Please use [http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template THIS TEMPLATE] to create project pages for this event.

==='''Neurosurgery, Brain and Spine, Traumatic Brain Injury'''===

# [[Semiautomatic longitudinal segmentation of MR volumes in traumatic brain injury]] (Andrei Irimia, Micah Chambers, Bo Wang, Marcel Prastawa, Danielle Pace, Stephen Aylward, Jack van Horn, Guido Gerig)
# [[2012_Summer_Project_Week:4D_Segmentation_TBI|4D Segmentation of longitudinal MRI of TBI patients]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig)
# [[2012_Summer_Project_Week:Intraoperative_Tract_Detection | Intraoperative White Matter Tract Detection Module]] (Lauren O'Donnell, Isaiah Norton)
# [[2012_Summer_Project_Week:Ultrasound_Aberration_Correction | An Ultrasound-based Method for Aberration Correction in TCFUS]] (Jason White, Greg Clement)
# [[2012_Summer_Project_Week:TimeSeriesMonitoringIntracranialBones| Monitoring time series images of intracranial bones in meningioma ]] (Karl Diedrich)
# [[2012_Summer_Project_Week:Early_Dementia_Diagnostic |Early Dementia Diagnostic Tools]] (Marcel Koek, Sonia Pujol)
# [[2012_Summer_Project_Week:Radnostics |Spine Segmentation & Osteoporosis Detection In CT Imaging Studies]] (Anthony Blumfield, Ron Kikinis)

==='''Radiation Therapy'''===
#[[2012_Summer_Project_Week:Atlas_based_segmentation_for_head_and_neck| Atlas-based segmentation for head and neck]] (Amelia Arbisser, Nadya Shusharina, James Shackleford, Greg Sharp, Polina Golland)
#[[2012_Summer_Project_Week:Overlapping_structures| First class structure set support in Slicer]] (Greg Sharp, James Shackleford, Steve Pieper)
#[[2012_Summer_Project_Week:PlastimatchIntegration| Plastimatch loadable module]] (James Shackleford, Greg Sharp)
#[[2012_Summer_Project_Week:Deformable_Registration_for_Head_and_Neck| Deformable Registration for Head and Neck ]] (Ivan Kolesov, Greg Sharp, Yi Gao, Allen Tannenbaum)
#[[2012_Summer_Project_Week:SlicerRT| Radiotherapy extensions for Slicer 4]] (Andras Lasso, Csaba Pinter, Kevin Wang)
#[[2012_Summer_Project_Week:PET_Image_Analysis | SUV Threshold Computation]] (Nadya Shusharina, Greg Sharp)

==='''Huntington's Disease'''===
# [[2012_Summer_Project_Week:Nipype Integration|Slicer/Nipype Integration]] (Hans Johnson)
# [[2012_Summer_Project_Week:DicomToNrrd|DicomToNrrdConverter Integration]] (Kent Williams, Hans Johnson)
# [[2012_Summer_Project_Week:4D shape analysis|4D Shape Analysis: Software Tools]] (James Fishbaugh, Marcel Prastawa, Guido Gerig)
# [[2012_Summer_Project_Week:DTI-Reg|DTI atlas based fiber analysis]] (Francois Budin)

==='''Atrial Fibrillation'''===
# [[2012_Summer_Project_Week:UtahCardiacRegistration|Cardiac MRI Registration Module]] (Greg Gardner, Alan Morris, Danny Perry, Josh Cates, Rob MacLeod)
# [[2012_Summer_Project_Week:UtahAutoScar|Automatic Left Atrial Scar Detection]] (Greg Gardner, Danny Perry, Alan Morris, Josh Cates, Rob MacLeod)
# [[2012_Summer_Project_Week:UtahInhomogeneity|MRI Inhomogeneity Correction Filter]] (Greg Gardner, Alan Morris, Eugene Kholmovski, Josh Cates, Danny Perry, Rob MacLeod)
# [[2012_Summer_Project_Week:VecReg|Vector-Valued Cardiac MRI Registration]] (Yi Gao, Josh Cates, Liang-Jia Zhu, Alan Morris, Danny Perry, Greg Gardner, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
# [[2012_Summer_Project_Week:RidgeExtractionAtrialWallSegmentation|Perceptual Ridge Extraction for Atrial Wall Segmentation in MRI]] (Arie Nakhmani, Allen Tannenbaum)

==='''Device Integration with Slicer and Image Guided Therapy'''===
# [[2012_Summer_Project_Week:SlicerWeb|Web Interface to Slicer 4]] (Steve Pieper)
# [[2012_Summer_Project_Week:OpenIGTLinkIF|Improvement of OpenIGTLink IF for Slicer 4]] (Junichi Tokuda, Laurent Chauvin)
# [[2012_Summer_Project_Week:LeanSlicer|Lean Slicer to facilitate regulatory approval]] (Andras Lasso, Chris Wedlake)
# [[2012_Summer_Project_Week:LiveUltrasound|Live Ultrasound]] (Tamas Ungi, Andinet Enquobahrie, Junichi Tokuda)
# [[2012_Summer_Project_Week:BK-PLUS_Integration|Integration of BK ProFocus US with Slicer via PLUS library]] (Andras Lasso, Andrey Fedorov, Isaiah Norton, Saman)
# [[2012_Summer_Project_Week:TransformRecorder|Transform Recorder and other IGT modules]] (Simrin Nagpal, Tamas Ungi)
# [[2012_Summer_Project_Week:Open_source_electromagnetic_trackers_using OpenIGTLink|Open-source electromagnetic trackers using OpenIGTLink]] (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)
# [[2012_Summer_Project_Week:iGyne|iGyne for Gynecological Cancer Brachytherapy]] (Xiaojun Chen, Jan Egger, Tina Kapur, Steve Pieper)
#[[2012_Summer_Project_Week:Interactive_Needle_Segmentation|Interactive Needle Segmentation for Gynecological Cancer Brachytherapy]] (Nabgha Farhat, Neha Agrawal, Jan Egger, Tina Kapur, Steve Pieper)
# [[2012_Summer_Project_Week:VertebraCTUSReg|Single Vertebra CT-US Registration]] (Samira Sojoudi, Saman Nouranian, Simrin Nagpal, Tamas Ungi, David Welch)
# [[2012_Summer_Project_Week:Fast Fiducial Registration|Fast Fiducial Registration Module]] (David Welch, Hans Johnson, Nicole Aucoin, Ron Kikinis)
# [[2012_Summer_Project_Week:SteeredRegistration|Steered Registration for Image Guided Therapy]] (Guillaume Pernelle BWH, Jan Egger, Tina Kapur, Steve Pieper, Jim Miller, Kunlin Cao)
# [[2012_Summer_Project_Week:4D_Ultrasound_Slicer4|4D Ultrasound on Slicer4]] (Laurent Chauvin, Nobuhiko Hata)
# [[2012_Summer_Project_Week:Kinect4Slicer|Kinect4Slicer]] (Laurent Chauvin, Nobuhiko Hata)
# [[2012_Summer_Project_Week:Needle Tip Tracking |Needle Tip Tracking for complex MR images]] (Atsushi Yamada, Nobuhiko Hata)

==='''General Segmentation'''===
#[[2012_Summer_Project_Week:SemiAutomatedAirwaySegmentationfrom0.64mmLungCTDatasets|Semi-automated airway segmentation from 0.64mm lung CT datasets]] (Pietro Nardelli, Padraig Cantillon-Murphy, Raul San Jose Estepar)
#[[Loading and segmentation of histopathology imaging for radiological-pathological correlation]] (Tobias Penzkofer, Andrey Fedorov)
#[[2012_Summer_Project_Week:ABC_Slicer4|Porting ABC extension to Slicer 4]] (Marcel Prastawa, Bo Wang, Guido Gerig)
# [[2012_Summer_Project_Week:QuantitativePETImageAnalysisModule|Quantitative PET Image Analysis Module]] (Markus Van Tol)
#[[2012_Summer_Project_Week:SegmentationWithLabelFusion|Segmentation with Label Fusion]] (Ramesh Sridharan, Christian Wachinger, Polina Golland)

==='''General Registration'''===
# [[2012_Summer_Project_Week:NiftyReg|NiftyReg integration]] (Marc Modat, Sonia Pujol)
#[[2012_Summer_Project_Week:ElastixIntegration|Elastix integration]] (Stefan Klein, Sonia Pujol)
# [[2012_Summer_Project_Week:DTIRegistration| Highly Deformable DTI Registration for cases with large pathological variations]] (Aditya Gupta, Martin Styner, Matthew Toews)
# [[2012_Summer_Project_Week:DifficultRegistration| Registration of Difficult Images]] (Matthew Toews, Stefan Klein, Marc Modat, Aditya Gupta, Martin Styner, Petter Risholm, Dominik Meier, William Wells)

==='''Informatics'''===
# [[2012_Summer_Project_Week:AIM_for_QIN|Applicability of AIM to QIN use cases]] (Andrey Fedorov, Reinhard Beichel, Jayashree Kalpathy-Cramer, Pat Mongkolwat, Daniel Rubin)
# [[2012_Summer_Project_Week:Reporting|Reporting module]] (Andrey, Nicole, Steve, Ron, Pat)
# [[2012_Summer_Project_Week:CMake_for_AIM_API|CMake-fying AIM API]] (Pat Mongklowat, Vlad Kleper, Andrey Fedorov)

==='''Infrastructure'''===

# [[2012_Summer_Project_Week:SelfTesting|Built-In Self-Testing (BIST) for Slicer]] (Steve, Julien, Jc, Sonia)
# [[2012_Summer_Project_Week:AnnotationModule|Annotation module redesign for Slicer]] (Nicole)
# [[2012_Summer_Project_Week:MultiVolumeSupport|Multivolume support]] (Andrey, Jim, Brendan Moloney)
# [[2012_Summer_Project_Week:PythonCLIandWidget|Python CLI modules (Demian, JC, Julien, Steve)]].
# [[2012_Summer_Project_Week:Charting|Charting]] (Jim)
# [[2012_Summer_Project_Week:GPUEditor|GPU Editor Effects]] (Steve, Jim)
# [[2012_Summer_Project_Week:XTK|XTK/WebGL Exporter]] (Daniel, Nicolas - Boston Children's Hospital)
# [[2012_Summer_Project_Week:EventOptimization|Callback/Events/Observation best practice + Performance bottleneck discussion (Julien, Steve,...)]]
# [[2012_Summer_Project_Week:XNATSlicerIntegration|XNAT/Slicer Integration]] (Sunil, Dan, Steve,...)
# [[2012_Summer_Project_Week:ITKv4 Integration|ITKv4 Integration]] (Hans Johnson, Julien Finet, Jim). See [http://www.na-mic.org/Bug/view.php?id=2007 #2007]
# [[2012_Summer_Project_Week:SimpleITK Integration|SimpleITK Integration]] (Hans Johnson, Bradley Lowekamp)
# [[2012_Summer_Project_Week:LongitudinalPETCTModule|Slicer Module for longitudinal analysis of PET-CT]] (Paul, Andriy, Ron, Markus,...)
# [[2012_Summer_Project_Week:Threat Modeling|Threat Modeling]] (JC, J2, Anthony)
# [[2012_Summer_Project_Week:CUDA Volume Rendering Extension|CUDA Volume Rendering as Extension]] (J2, Elvis)

==Background==

We are pleased to announce the 15th PROJECT WEEK of hands-on research and development activity for applications in Neuroscience, Image-Guided Therapy and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants. If you would like to learn more about this event, please [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week click here to join our mailing list].

Active preparation begins on Thursday, April 26th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 40-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], [http://www.cimit.org CIMIT], and OCAIRO. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].

== Logistics ==
*'''Dates:''' June 18-22, 2012.
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''REGISTRATION:''' Please click [https://www.regonline.com/namic2012summerprojweek HERE] to do an on-line registration for the meeting that will allow you to pay by credit card. No checks will be accepted.
*'''Registration Fee:''' $300 (covers the cost of breakfast, lunch and coffee breaks for the week).
*'''Hotel:''' No room blocks have been reserved in any area hotel. Please select a [http://web.mit.edu/institute-events/visitor/stay.html hotel of your choice] and make reservations as early as possible. Some area hotels are:
**marriott cambridge center
**marriott residence inn kendall square
**le meridien central square
**hotel marlowe cambridge
**royal sonesta hotel cambridge

== Preparation ==
# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 26, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on Thursday May 10, all participants to add a one line title of their project to #Projects
# By 3pm ET on Thursday June 7, all project leads to complete [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 14: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Matt)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Where possible, setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Matt)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## See the [http://www.slicer.org/slicerWiki/index.php/Documentation/4.0/Developers Developer Section of slicer.org] for information.
## Projects to develop extension modules should be built against the latest Slicer4 trunk.

==Registrants==

Do not add your name to this list- it is maintained by the organizers based on your paid registration. ([http://www.regonline.com/Register/Checkin.aspx?EventID=1089602 Please click here to register.])

#Anderson, Peter, retired, traneus@verizon.net
#Arbisser, Amelia, MIT, arbisser@mit.edu
#Aucoin, Nicole, BWH, Nicole@bwh.harvard.edu
#Aylward, Stephen, Kitware, stephen.aylward@kitware.com
#Blevins, Scott, BWH, stblevins@gmail.com
#Blumfield, Anthony, Radnostics, Anthony.Blumfield@Radnostics.com
#Budin, Francis, NIRAL-UNC, fbudin@unc.edu
#Cao, Kunlin, GE Research, cao@ge.com
#Chambers, Micah, UCLA, micahcc@ucla.edu
#Chauvin, Laurent, SPL, lchauvin@bwh.harvard.edu
#Chen, Elvis, Robarts, chene@robarts.ca
#Chen, Xiaojun, SPL, xiaojun@bwh.harvard.edu
#Datar, Manasi, Utah SCI, datar@sci.utah.edu
#Diedrich, Karl, AZE R&D, karl.diedrich@azeresearch.com
#Egger, Jan, BWH, egger@bwh.harvard.edu
#Farhat, Nabgha, SPL, nfarhat@bwh.harvard.edu
#Fedorov, Andriy, BWH, fedorov@bwh.harvard.edu
#Fillion-Robin, Jean-Christophe, Kitware, jchris.fillionr@kitware.com
#Finet, Julien, Kitware, julien.finet@kitware.com
#Fishbaugh, James, SCI, jfishbau@sci.utah.edu
#Gao, Yi, BWH, gaoyi@bwh.harvard.edu
#Gardner, Greg, SCI, ggardner@sci.utah.edu
#Golland, Polina, MIT CSAIL, polina@csail.mit.edu
#Gouaillard, Alexandre, A*STAR, agouaillard@gmail.com
#Gupta, Aditya, NIRAL UNC, aditya_gupta@med.unc.edu
#Irimia, Andrei, UCLA, andrei.irimia@loni.ucla.edu
#Jagadeesan, Jayender, SPL, jayender@bwh.harvard.edu
#Johnson, Hans, Univ Iowa, hans-johnson@uiowa.edu
#Kalpathy-Cramer, Jayashree, MGH, kalpathy@nmr.mgh.harvard.edu
#Kapur, Tina, BWH HMS, tkapur@bwh.harvard.edu
#Kikinis, Ron, HMS, kikinis@bwh.harvard.edu
#Klein, Stefan, (cancelled registration) Erasmus MC, s.klein@erasmusmc.nl
#Kleper, Vladimir, Northwestern Univ, vkleper@northwestern.edu
#Koek, Marcel, Erasmus MC, m.koek@erasmusmc.nl
#Kolesov, Ivan, GA Tech, ivan.kolesov@gatech.edu
#Kumar, Sunil, Washington Univ St Louis, kumars@mir.wustl.edu
#Lasso, Andras, Queen's Univ, lasso@cs.queensu.ca
#Lowekamp, Bradley, NLM/NIH, bradley.lowekamp@nih.gov
#Macule, Raul, AZE R&D, raul.macule@azeresearch.com
#Mastrogiacomo, Katie, SPL, BWH, kmast@bwh.harvard.edu
#Meier, Dominik, BWH, meier@bwh.harvard.edu
#Mercea, Paul, SPL, pmercea@bwh.harvard.edu
#Miller, Jim, GE Research, millerjv@ge.com
#Mizutani, Tatsushi, Nagoya Univ, tatsushi0207@me.com
#Modat, Marc, Univ College London, m.modat@ucl.ac.uk
#Moloney, Brendan, AIRC, moloney.brendan@gmail.com
#Mongkolwat, Pattanasak, Northwestern U, p-mongkolwat@northwestern.edu
#Montillo, Albert, GE Research, montillo@ge.com
#Nagpal, Simrin, Queen’s Univ, 7sn6@cs.queensu.ca
#Nakhmani, Arie, BU, nakhmani@gmail.com
#Nardelli, Pietro, Univ College Cork, pie.nardelli@gmal.com
#Norton, Isaiah, BWH, inorton@partners.org
#Nouranian, Saman, Univ BC, samann@ece.ubc.ca
#O'Donnell, Lauren, BWH, odonnell@bwh.harvard.edu
#Oyama, Rie, BWH, royama@bwh.harvard.edu
#Paniagua, Beatriz, Univ NC Chapel Hill, bpaniagua@gmail.com
#Penzkofer, Tobias, SPL, pt@bwh.harvard.edu
#Pernelle, Guillaume, BWH, gpernelle@gmail.com
#Pieper, Steve, Isomics, pieper@bwh.harvard.edu
#Pinter, Csaba, Queen's Univ, pinter@cs.queensu.ca
#Pujol, Sonia, BWH, spujol@bwh.harvard.edu
#Rannou, Nicolas, Childrens Hospital, nicolas.rannou@childrens.harvard.edu
#Razzaque, Sharif, InnerOptic Technology, sharif@inneroptic.com
#Risholm, Petter, Harvard, pettri@bwh.harvard.edu
#San Jose, Raul, BWH, rjosest@bwh.harvard.edu
#Schroeder, William, Kitware, will.schroeder@kitware.com
#Shackleford, James, MGH, jshackleford@partners.org
#Sharp, Greg, MGH, gcsharp@partners.org
#Shusharina, Nadya, MGH, nshusharina@partners.org
#Sojoudi, Samira, Univ BC, samiras@ece.ubc.ca
#Spindler, Wolf, Fraunhofer MEVIS, wolf.spindler@mevis.fraunhofer.de
#Sridharan, Ramesh, MIT CSAIL, rameshvs@MIT.EDU
#State, Andrei, InnerOptic Technology, andrei@inneroptic.com
#Tiwari, Pallavi, Rutgers, pallavi.tiwar@gmail.com
#Toews, Matthew, BWH HMS, mt@bwh.harvard.edu
#Tokuda, Junichi, BWH, tokuda@bwh.harvard.edu
#Ungi, Tamas, Queen's Univ, ungi@cs.queensu.ca
#Van Tol, Markus, Univ Iowa, mvantol@engineering.uiowa.edu
#Vosburgh, Kirby, BWH, kirby@bwh.harvard.edu
#Wang, Bo, SCI, bowang@sci.utah.edu
#Wang, Kevin, Princess Margaret Hospital, kevin.wang@rmp.uhn.on.ca
#Wedlake, Chris, Robarts, cwedlake@robarts.ca
#Welch, David, Univ Iowa, david-welch@uiowa.edu
#Wells, William, HMS BWH, sw@bwh.harvard.edu
#Whitaker, Ross, SCI, whitaker@cs.utah.edu
#White, Phillip, BWH HMS, white@bwh.harvard.edu
#Yamada, Atsushi, BWH, ayamada@bwh.harvard.edu
#Yarmakovich, Alex, Isomics, alexy@bwh.harvard.edu

2012 Summer Project Week

2012-06-18T16:58:32Z

Hjmjohnson: /* Infrastructure */

Back to [[Events]]

[[image:PW-MIT2012.png|200px]]

*'''Dates:''' June 18-22, 2012
*'''Location:''' MIT

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 18
!style="width:18%" |Tuesday, June 19
!style="width:18%" |Wednesday, June 20
!style="width:18%" |Thursday, June 21
!style="width:18%" |Friday, June 22
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''9am-10am:''' What's new in Slicer4 (Charts - Jim, DICOM - Steve) <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
<br>----------------------------------------<br>
'''10-11am''' Slicer4 Python Q&A <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
|'''9am-11pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2012 Project Week Breakout Session: SimpleITK|Slicer and SimpleITK]] (Hans)
[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
<br>----------------------------------------<br>
'''10am-12pm: <font color="#4020ff">Computation Core PIs: closed meeting with Ron:'''</font><br>
[[MIT_Project_Week_Rooms#Star|Star Room]]
|'''9am-12pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2012 Summer Project Week Breakout Session:Slicer in Networked Environment|Slicer in Networked Environment]] (Junichi)
[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-4:30pm''' [[2012 Summer Project Week Breakout Session:SlicerExtensions|Slicer4 Extensions]] (JC) <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]
|'''3-4pm:''' [[2012_Tutorial_Contest|Tutorial Contest Presentations]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''4-5pm:''' Breakout Session: DICOM, Networking, RT, Segmentations (Steve, Greg, Andras, Andre)
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''12:45-1pm:''' [[Events:TutorialContestJune2012|Tutorial Contest Winner Announcement]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3-30pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2012 Summer Project Week Breakout Session:QtTesting|QtTesting]] (JC)
|'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2012 Summer Project Week Breakout Session:Ultrasound|Ultrasound]] (Tamas)
[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

==Projects==

Please use [http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template THIS TEMPLATE] to create project pages for this event.

==='''Neurosurgery, Brain and Spine, Traumatic Brain Injury'''===

# [[Semiautomatic longitudinal segmentation of MR volumes in traumatic brain injury]] (Andrei Irimia, Micah Chambers, Bo Wang, Marcel Prastawa, Danielle Pace, Stephen Aylward, Jack van Horn, Guido Gerig)
# [[2012_Summer_Project_Week:4D_Segmentation_TBI|4D Segmentation of longitudinal MRI of TBI patients]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig)
# [[2012_Summer_Project_Week:Intraoperative_Tract_Detection | Intraoperative White Matter Tract Detection Module]] (Lauren O'Donnell, Isaiah Norton)
# [[2012_Summer_Project_Week:Ultrasound_Aberration_Correction | An Ultrasound-based Method for Aberration Correction in TCFUS]] (Jason White, Greg Clement)
# [[2012_Summer_Project_Week:TimeSeriesMonitoringIntracranialBones| Monitoring time series images of intracranial bones in meningioma ]] (Karl Diedrich)
# [[2012_Summer_Project_Week:Early_Dementia_Diagnostic |Early Dementia Diagnostic Tools]] (Marcel Koek, Sonia Pujol)
# [[2012_Summer_Project_Week:Radnostics |Spine Segmentation & Osteoporosis Detection In CT Imaging Studies]] (Anthony Blumfield, Ron Kikinis)

==='''Radiation Therapy'''===
#[[2012_Summer_Project_Week:Atlas_based_segmentation_for_head_and_neck| Atlas-based segmentation for head and neck]] (Amelia Arbisser, Nadya Shusharina, James Shackleford, Greg Sharp, Polina Golland)
#[[2012_Summer_Project_Week:Overlapping_structures| First class structure set support in Slicer]] (Greg Sharp, James Shackleford, Steve Pieper)
#[[2012_Summer_Project_Week:PlastimatchIntegration| Plastimatch loadable module]] (James Shackleford, Greg Sharp)
#[[2012_Summer_Project_Week:Deformable_Registration_for_Head_and_Neck| Deformable Registration for Head and Neck ]] (Ivan Kolesov, Greg Sharp, Yi Gao, Allen Tannenbaum)
#[[2012_Summer_Project_Week:SlicerRT| Radiotherapy extensions for Slicer 4]] (Andras Lasso, Csaba Pinter, Kevin Wang)
#[[2012_Summer_Project_Week:PET_Image_Analysis | SUV Threshold Computation]] (Nadya Shusharina, Greg Sharp)

==='''Huntington's Disease'''===
# [[2012_Summer_Project_Week:DTIPrep|DTIPrep]] (David Welch, Hans Johnson)
# [[2012_Summer_Project_Week:ANTS Registation|ANTS Registation Module]] (David Welch, Hans Johnson)
# [[2012_Summer_Project_Week:Nipype Integration|Slicer/Nipype Integration]] (Hans Johnson)
# [[2012_Summer_Project_Week:DicomToNrrd|DicomToNrrdConverter Integration]] (Kent Williams)
# [[2012_Summer_Project_Week:4D shape analysis|4D Shape Analysis: Software Tools]] (James Fishbaugh, Marcel Prastawa, Guido Gerig)
# [[2012_Summer_Project_Week:DTI-Reg|DTI atlas based fiber analysis]] (Francois Budin)

==='''Atrial Fibrillation'''===
# [[2012_Summer_Project_Week:UtahCardiacRegistration|Cardiac MRI Registration Module]] (Alan Morris, Danny Perry, Josh Cates, Greg Gardner, Rob MacLeod)
# [[2012_Summer_Project_Week:UtahAutoScar|Automatic Left Atrial Scar Detection]] (Danny Perry, Alan Morris, Josh Cates, Rob MacLeod)
# [[2012_Summer_Project_Week:UtahInhomogeneity|MRI Inhomogeneity Correction Filter]] (Alan Morris, Eugene Kholmovski, Josh Cates, Danny Perry, Rob MacLeod)
# [[2012_Summer_Project_Week:VecReg|Vector-Valued Cardiac MRI Registration]] (Yi Gao, Josh Cates, Liang-Jia Zhu, Alan Morris, Danny Perry, Greg Gardner, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
# [[2012_Summer_Project_Week:RidgeExtractionAtrialWallSegmentation|Perceptual Ridge Extraction for Atrial Wall Segmentation in MRI]] (Arie Nakhmani, Allen Tannenbaum)

==='''Device Integration with Slicer and Image Guided Therapy'''===
# [[2012_Summer_Project_Week:SlicerWeb|Web Interface to Slicer 4]] (Steve Pieper)
# [[2012_Summer_Project_Week:OpenIGTLinkIF|Improvement of OpenIGTLink IF for Slicer 4]] (Junichi Tokuda)
# [[2012_Summer_Project_Week:LeanSlicer|Lean Slicer to facilitate regulatory approval]] (Andras Lasso, Chris Wedlake)
# [[2012_Summer_Project_Week:LiveUltrasound|Live Ultrasound]] (Tamas Ungi, Andinet Enquobahrie, Junichi Tokuda)
# [[2012_Summer_Project_Week:BK-PLUS_Integration|Integration of BK ProFocus US with Slicer via PLUS library]] (Andras Lasso, Andrey Fedorov, Isaiah Norton, Saman)
# [[2012_Summer_Project_Week:TransformRecorder|Transform Recorder and other IGT modules]] (Simrin Nagpal, Tamas Ungi)
# [[2012_Summer_Project_Week:Open_source_electromagnetic_trackers_using OpenIGTLink|Open-source electromagnetic trackers using OpenIGTLink]] (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)
# [[2012_Summer_Project_Week:iGyne|iGyne for Gynecological Cancer Brachytherapy]] (Xiaojun Chen, Jan Egger, Tina Kapur, Steve Pieper)
#[[2012_Summer_Project_Week:Interactive_Needle_Segmentation|Interactive Needle Segmentation for Gynecological Cancer Brachytherapy]] (Nabgha Farhat, Neha Agrawal, Jan Egger, Tina Kapur, Steve Pieper)
# [[2012_Summer_Project_Week:VertebraCTUSReg|Single Vertebra CT-US Registration]] (Samira Sojoudi, Saman Nouranian, Simrin Nagpal, Tamas Ungi, David Welch)
# [[2012_Summer_Project_Week:Fast Fiducial Registration|Fast Fiducial Registration Module]] (David Welch, Hans Johnson, Nicole Aucoin, Ron Kikinis)
# [[2012_Summer_Project_Week:SteeredRegistration|Steered Registration for Image Guided Therapy]] (Guillaume Pernelle BWH, Jan Egger, Tina Kapur, Steve Pieper, Jim Miller, Kunlin Cao)
# [[2012_Summer_Project_Week:4D_Ultrasound_Slicer4|4D Ultrasound on Slicer4]] (Laurent Chauvin, Nobuhiko Hata)
# [[2012_Summer_Project_Week:Kinect4Slicer|Kinect4Slicer]] (Laurent Chauvin, Nobuhiko Hata)
# [[2012_Summer_Project_Week:Needle Tip Tracking |Needle Tip Tracking for complex MR images]] (Atsushi Yamada, Nobuhiko Hata)

==='''General Segmentation'''===
#[[2012_Summer_Project_Week:SemiAutomatedAirwaySegmentationfrom0.64mmLungCTDatasets|Semi-automated airway segmentation from 0.64mm lung CT datasets]] (Pietro Nardelli, Padraig Cantillon-Murphy, Raul San Jose Estepar)
#[[Loading and segmentation of histopathology imaging for radiological-pathological correlation]] (Andrey Fedorov, Tobias Penzkofer)
#[[2012_Summer_Project_Week:ABC_Slicer4|Porting ABC extension to Slicer 4]] (Marcel Prastawa, Bo Wang, Guido Gerig)
# [[2012_Summer_Project_Week:QuantitativePETImageAnalysisModule|Quantitative PET Image Analysis Module]] (Markus Van Tol)
#[[2012_Summer_Project_Week:SegmentationWithLabelFusion|Segmentation with Label Fusion]] (Ramesh Sridharan, Christian Wachinger, Polina Golland)

==='''General Registration'''===
# [[2012_Summer_Project_Week:NiftyReg|NiftyReg integration]] (Marc Modat, Sonia Pujol)
#[[2012_Summer_Project_Week:ElastixIntegration|Elastix integration]] (Stefan Klein, Sonia Pujol)
# [[2012_Summer_Project_Week:DTIRegistration| Highly Deformable DTI Registration for cases with large pathological variations]] (Aditya Gupta, Martin Styner, Matthew Toews)
# [[2012_Summer_Project_Week:DifficultRegistration| Registration of Difficult Images]] (Matthew Toews, Stefan Klein, Marc Modat, Aditya Gupta, Martin Styner, Petter Risholm, Dominik Meier, William Wells)

==='''Informatics'''===
# [[2012_Summer_Project_Week:AIM_for_QIN|Applicability of AIM to QIN use cases]] (Andrey Fedorov, Reinhard Beichel, Jayashree Kalpathy-Cramer, Pat Mongkolwat, Daniel Rubin)
# [[2012_Summer_Project_Week:Reporting|Reporting module]] (Andrey, Nicole, Steve, Ron, Pat)

==='''Infrastructure'''===

# [[2012_Summer_Project_Week:SelfTesting|Built-In Self-Testing (BIST) for Slicer]] (Steve, Julien, Jc, Sonia)
# [[2012_Summer_Project_Week:AnnotationModule|Annotation module redesign for Slicer]] (Nicole)
# [[2012_Summer_Project_Week:MultiVolumeSupport|Multivolume support]] (Andrey, Jim, Brendan Moloney)
# [[2012_Summer_Project_Week:PythonCLIandWidget|Python CLI modules (Demian, JC, Julien, Steve)]].
# [[2012_Summer_Project_Week:Charting|Charting]] (Jim)
# [[2012_Summer_Project_Week:GPUEditor|GPU Editor Effects]] (Steve, Jim)
# [[2012_Summer_Project_Week:XTK|XTK/WebGL Exporter]] (Daniel, Nicolas - Boston Children's Hospital)
# [[2012_Summer_Project_Week:EventOptimization|Callback/Events/Observation best practice + Performance bottleneck discussion (Julien, Steve,...)]]
# [[2012_Summer_Project_Week:XNATSlicerIntegration|XNAT/Slicer Integration]] (Sunil, Dan, Steve,...)
# [[2012_Summer_Project_Week:ITKv4 Integration|ITKv4 Integration]] (Hans Johnson, Julien Finet, Jim). See [http://www.na-mic.org/Bug/view.php?id=2007 #2007]
# [[2012_Summer_Project_Week:SimpleITK Integration|SimpleITK Integration]] (Hans Johnson, Bradley Lowekamp)
# [[2012_Summer_Project_Week:LongitudinalPETCTModule|Slicer Module for longitudinal analysis of PET-CT]] (Paul, Andriy, Ron, Markus,...)
# [[2012_Summer_Project_Week:Threat Modeling|Threat Modeling]] (JC, J2, Anthony)

==Background==

We are pleased to announce the 15th PROJECT WEEK of hands-on research and development activity for applications in Neuroscience, Image-Guided Therapy and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants. If you would like to learn more about this event, please [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week click here to join our mailing list].

Active preparation begins on Thursday, April 26th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 40-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], [http://www.cimit.org CIMIT], and OCAIRO. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].

== Logistics ==
*'''Dates:''' June 18-22, 2012.
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''REGISTRATION:''' Please click [https://www.regonline.com/namic2012summerprojweek HERE] to do an on-line registration for the meeting that will allow you to pay by credit card. No checks will be accepted.
*'''Registration Fee:''' $300 (covers the cost of breakfast, lunch and coffee breaks for the week).
*'''Hotel:''' No room blocks have been reserved in any area hotel. Please select a [http://web.mit.edu/institute-events/visitor/stay.html hotel of your choice] and make reservations as early as possible. Some area hotels are:
**marriott cambridge center
**marriott residence inn kendall square
**le meridien central square
**hotel marlowe cambridge
**royal sonesta hotel cambridge

== Preparation ==
# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 26, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on Thursday May 10, all participants to add a one line title of their project to #Projects
# By 3pm ET on Thursday June 7, all project leads to complete [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 14: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Matt)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Where possible, setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Matt)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## See the [http://www.slicer.org/slicerWiki/index.php/Documentation/4.0/Developers Developer Section of slicer.org] for information.
## Projects to develop extension modules should be built against the latest Slicer4 trunk.

==Registrants==

Do not add your name to this list- it is maintained by the organizers based on your paid registration. ([http://www.regonline.com/Register/Checkin.aspx?EventID=1089602 Please click here to register.])

#Anderson, Peter, retired, traneus@verizon.net
#Arbisser, Amelia, MIT, arbisser@mit.edu
#Aucoin, Nicole, BWH, Nicole@bwh.harvard.edu
#Aylward, Stephen, Kitware, stephen.aylward@kitware.com
#Blevins, Scott, BWH, stblevins@gmail.com
#Blumfield, Anthony, Radnostics, Anthony.Blumfield@Radnostics.com
#Budin, Francis, NIRAL-UNC, fbudin@unc.edu
#Cao, Kunlin, GE Research, cao@ge.com
#Chambers, Micah, UCLA, micahcc@ucla.edu
#Chauvin, Laurent, SPL, lchauvin@bwh.harvard.edu
#Chen, Elvis, Robarts, chene@robarts.ca
#Chen, Xiaojun, SPL, xiaojun@bwh.harvard.edu
#Datar, Manasi, Utah SCI, datar@sci.utah.edu
#Diedrich, Karl, AZE R&D, karl.diedrich@azeresearch.com
#Egger, Jan, BWH, egger@bwh.harvard.edu
#Farhat, Nabgha, SPL, nfarhat@bwh.harvard.edu
#Fedorov, Andriy, BWH, fedorov@bwh.harvard.edu
#Fillion-Robin, Jean-Christophe, Kitware, jchris.fillionr@kitware.com
#Finet, Julien, Kitware, julien.finet@kitware.com
#Fishbaugh, James, SCI, jfishbau@sci.utah.edu
#Gao, Yi, BWH, gaoyi@bwh.harvard.edu
#Gardner, Greg, SCI, ggardner@sci.utah.edu
#Golland, Polina, MIT CSAIL, polina@csail.mit.edu
#Gouaillard, Alexandre, A*STAR, agouaillard@gmail.com
#Gupta, Aditya, NIRAL UNC, aditya_gupta@med.unc.edu
#Jagadeesan, Jayender, SPL, jayender@bwh.harvard.edu
#Johnson, Hans, Univ Iowa, hans-johnson@uiowa.edu
#Kalpathy-Cramer, Jayashree, MGH, kalpathy@nmr.mgh.harvard.edu
#Kapur, Tina, BWH HMS, tkapur@bwh.harvard.edu
#Kikinis, Ron, HMS, kikinis@bwh.harvard.edu
#Klein, Stefan, Erasmus MC, s.klein@erasmusmc.nl
#Kleper, Vladimir, Northwestern Univ, vkleper@northwestern.edu
#Koek, Marcel, Erasmus MC, m.koek@erasmusmc.nl
#Kolesov, Ivan, GA Tech, ivan.kolesov@gatech.edu
#Kumar, Sunil, Washington Univ St Louis, kumars@mir.wustl.edu
#Lasso, Andras, Queen's Univ, lasso@cs.queensu.ca
#Lowekamp, Bradley, NLM/NIH, bradley.lowekamp@nih.gov
#Macule, Raul, AZE R&D, raul.macule@azeresearch.com
#Mastrogiacomo, Katie, SPL, BWH, kmast@bwh.harvard.edu
#Meier, Dominik, BWH, meier@bwh.harvard.edu
#Mercea, Paul, SPL, pmercea@bwh.harvard.edu
#Miller, Jim, GE Research, millerjv@ge.com
#Mizutani, Tatsushi, Nagoya Univ, tatsushi0207@me.com
#Modat, Marc, Univ College London, m.modat@ucl.ac.uk
#Moloney, Brendan, AIRC, moloney.brendan@gmail.com
#Mongkolwat, Pattanasak, Northwestern U, p-mongkolwat@northwestern.edu
#Montillo, Albert, GE Research, montillo@ge.com
#Nagpal, Simrin, Queen’s Univ, 7sn6@cs.queensu.ca
#Nakhmani, Arie, BU, nakhmani@gmail.com
#Nardelli, Pietro, Univ College Cork, pie.nardelli@gmal.com
#Norton, Isaiah, BWH, inorton@partners.org
#Nouranian, Saman, Univ BC, samann@ece.ubc.ca
#O'Donnell, Lauren, BWH, odonnell@bwh.harvard.edu
#Oyama, Rie, BWH, royama@bwh.harvard.edu
#Paniagua, Beatriz, Univ NC Chapel Hill, bpaniagua@gmail.com
#Penzkofer, Tobias, SPL, pt@bwh.harvard.edu
#Pernelle, Guillaume, BWH, gpernelle@gmail.com
#Pieper, Steve, Isomics, pieper@bwh.harvard.edu
#Pinter, Csaba, Queen's Univ, pinter@cs.queensu.ca
#Pujol, Sonia, BWH, spujol@bwh.harvard.edu
#Rannou, Nicolas, Childrens Hospital, nicolas.rannou@childrens.harvard.edu
#Razzaque, Sharif, InnerOptic Technology, sharif@inneroptic.com
#Risholm, Petter, Harvard, pettri@bwh.harvard.edu
#San Jose, Raul, BWH, rjosest@bwh.harvard.edu
#Schroeder, William, Kitware, will.schroeder@kitware.com
#Shackleford, James, MGH, jshackleford@partners.org
#Sharp, Greg, MGH, gcsharp@partners.org
#Shusharina, Nadya, MGH, nshusharina@partners.org
#Sojoudi, Samira, Univ BC, samiras@ece.ubc.ca
#Spindler, Wolf, Fraunhofer MEVIS, wolf.spindler@mevis.fraunhofer.de
#Sridharan, Ramesh, MIT CSAIL, rameshvs@MIT.EDU
#State, Andrei, InnerOptic Technology, andrei@inneroptic.com
#Tiwari, Pallavi, Rutgers, pallavi.tiwar@gmail.com
#Toews, Matthew, BWH HMS, mt@bwh.harvard.edu
#Tokuda, Junichi, BWH, tokuda@bwh.harvard.edu
#Ungi, Tamas, Queen's Univ, ungi@cs.queensu.ca
#Van Tol, Markus, Univ Iowa, mvantol@engineering.uiowa.edu
#Vosburgh, Kirby, BWH, kirby@bwh.harvard.edu
#Wang, Bo, SCI, bowang@sci.utah.edu
#Wang, Kevin, Princess Margaret Hospital, kevin.wang@rmp.uhn.on.ca
#Wedlake, Chris, Robarts, cwedlake@robarts.ca
#Welch, David, Univ Iowa, david-welch@uiowa.edu
#Whitaker, Ross, SCI, whitaker@cs.utah.edu
#White, Phillip, BWH HMS, white@bwh.harvard.edu
#Yamada, Atsushi, BWH, ayamada@bwh.harvard.edu
#Yarmakovich, Alex, Isomics, alexy@bwh.harvard.edu

2012 Summer Project Week:Nipype Integration

2012-06-18T16:48:55Z

Hjmjohnson:

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:BAW.png
</gallery>

==Key Investigators==
* UIowa: Hans Johnson

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
Nipype is a flexible, uniform interface to existing neuroimaging software that allows interaction between these packages within a single workflow. Our objective is to improve on Nipype's interaction with Slicer, with the goal of being able to pass scripts to Slicer's python interface that allow pipeline development within Slicer.
</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
# Meet with Satra
# Discuss python environment with JC and Steve and others
# Determine how python modules can be more easily incorporated with Slicer
# Investigate updates to Numpy and Scipy

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
SlicerCLI modules created and wrapped with nipype outside of Slicer
</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline
##Extension -- loadable
#Other (Please specify)

==References==
* Nipype: http://nipy.sourceforge.net/nipype/ [http://nipy.sourceforge.net/nipype/]
* Consider merging the [https://github.com/pieper/Slicer/tree/syspy system python] changes as a way to give easy access.
* Consider bundling python executable with slicer to simplify installation of python packages.

File:BAW.png

2012-06-18T16:45:46Z

Hjmjohnson: BAW representative example.

BAW representative example.

File:BAW WROKUP.png

2012-06-18T16:40:59Z

Hjmjohnson: This is a picture of the workflow for BAW.

This is a picture of the workflow for BAW.

2012 Project Week Breakout Session: SimpleITK

2012-06-18T16:30:34Z

Hjmjohnson:

This session will focus on demonstrating how to use SimpleITK with Slicer.

# How to compile Slicer for SimpleITK integration
# How to build a CLI module with SimpleITK
# How to pass images to/from Slicer in python

<pre>
import SimpleITK as sitk
import sitkUtils as su
help(su.PullFromSlicer)
# PullFromSlicer(NodeName)
# Given a slicer MRML image name, return the SimpleITK image object.
help(su.PushToSlicer)
# PushToSlicer(sitkimage, NodeName, makeBackgroundImage=False)
# Given a SimpleITK image, push it back to slicer for viewing
help(sitk.OtsuThreshold)
# OtsuThreshold(Image image, uint8_t inInsideValue = 1u,
# uint8_t inOutsideValue = 0u,
# uint32_t inNumberOfHistogramBins = 128u) -> Image
help(sitk.Cast)
help(sitk.CannyEdgeDetection)
help(sitk.SobelEdgeDetection)
mrhead=su.PullFromSlicer("MRHead")
mrhead.GetDirection()
mrhead.GetSpacing()
mrhead.GetOrigin()
mask=sitk.OtsuThreshold(mrhead,1,0)
su.PushToSlicer(mask,"MyMask",1)
def MakeOutline(FillSize):
dilate=sitk.DilateObjectMorphology(mask,FillSize)
erode=sitk.ErodeObjectMorphology(dilate,FillSize)
float_image=sitk.Cast(erode,sitk.sitkFloat32)
edge=sitk.SobelEdgeDetection(float_image)
return edge
edge=MakeOutline(7)
su.PushToSlicer(edge,"Edge",1)
PointSource=sitk.Image(64,64,64,sitk.sitkFloat32)
PointSource[31,31,31]=100
for sigma in range(1,9,3):
gsmooth=sitk.RecursiveGaussian(PointSource,sigma)
su.PushToSlicer(gsmooth,"GaussSmooth"+str(sigma),True)
</pre>

2012 Summer Project Week:ITKv4 Integration

2012-06-07T19:35:43Z

Hjmjohnson:

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Iowa: Hans Johnson, Kent Williams
* GE: Jim Miller
* SPL: Steve Pieper
* Kitware: JC, Julien

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
Move Slicer from ITKv3 to ITKv4
</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
Figure out how to get packaging working when building with ITKv4
</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
Basic building is working (Has been for a long time).
</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

As part of the CMake build system

==References==

</div>

2012 Summer Project Week:SimpleITK Integration

2012-06-07T19:32:51Z

Hjmjohnson:

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Iowa: Hans Johnson
* NLM: Bradley Lowekamp

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
Seemlessly integrate SimpleITK into Slicer

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>

Need to decide how to best integrate SimpleITK. Just an External project, an integral part, a compile time option.

There are several options that have been discussed. We need to determine which approach to take.

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
Preliminary work has been done.

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline
##Extension -- loadable
#Other (Please specify)

==References==
</div>

2012 Summer Project Week:SimpleITK Integration

2012-06-07T19:30:09Z

Hjmjohnson: /* Instructions for Use of this Template */

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.
Image:genuFA.jpg|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.
</gallery>

==Key Investigators==
* UNC: Isabelle Corouge, Casey Goodlett, Guido Gerig
* Utah: Tom Fletcher, Ross Whitaker

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
We are developing methods for analyzing diffusion tensor data along fiber tracts. The goal is to be able to make statistical group comparisons with fiber tracts as a common reference frame for comparison.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>

Our approach for analyzing diffusion tensors is summarized in the IPMI 2007 reference below. The main challenge to this approach is <foo>.

Our plan for the project week is to first try out <bar>,...

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
Software for the fiber tracking and statistical analysis along the tracts has been implemented. The statistical methods for diffusion tensors are implemented as ITK code as part of the [[NA-MIC/Projects/Diffusion_Image_Analysis/DTI_Software_and_Algorithm_Infrastructure|DTI Software Infrastructure]] project. The methods have been validated on a repeated scan of a healthy individual. This work has been published as a conference paper (MICCAI 2005) and a journal version (MEDIA 2006). Our recent IPMI 2007 paper includes a nonparametric regression method for analyzing data along a fiber tract.

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline
##Extension -- loadable
#Other (Please specify)

==References==
*Fletcher P, Tao R, Jeong W, Whitaker R. [http://www.na-mic.org/publications/item/view/634 A volumetric approach to quantifying region-to-region white matter connectivity in diffusion tensor MRI.] Inf Process Med Imaging. 2007;20:346-358. PMID: 17633712.
* Corouge I, Fletcher P, Joshi S, Gouttard S, Gerig G. [http://www.na-mic.org/publications/item/view/292 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Med Image Anal. 2006 Oct;10(5):786-98. PMID: 16926104.
* Corouge I, Fletcher P, Joshi S, Gilmore J, Gerig G. [http://www.na-mic.org/publications/item/view/1122 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Int Conf Med Image Comput Comput Assist Interv. 2005;8(Pt 1):131-9. PMID: 16685838.
* Goodlett C, Corouge I, Jomier M, Gerig G, A Quantitative DTI Fiber Tract Analysis Suite, The Insight Journal, vol. ISC/NAMIC/ MICCAI Workshop on Open-Source Software, 2005, Online publication: http://hdl.handle.net/1926/39 .

</div>

2012 Summer Project Week:Nipype Integration

2012-06-07T19:27:05Z

Hjmjohnson: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* UIowa: Hans Johnson

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
Nipype is a flexible, uniform interface to existing neuroimaging software that allows interaction between these packages within a single workflow. Our objective is to improve on Nipype's interaction with Slicer, with the goal of being able to pass scripts to Slicer's python interface that allow pipeline development within Slicer.
</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
Meet with Satra
Discuss python environment with JC and Steve
Investigate updates to Numpy and Scipy

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
N/A

</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline
##Extension -- loadable
#Other (Please specify)

==References==
* Nipype: http://nipy.sourceforge.net/nipype/ [http://nipy.sourceforge.net/nipype/]

2012 Summer Project Week

2012-06-06T14:18:29Z

Hjmjohnson: /* Agenda */

Back to [[Events]]

[[image:PW-MIT2012.png|200px]]

*'''Dates:''' June 18-22, 2012
*'''Location:''' MIT

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 18
!style="width:18%" |Tuesday, June 19
!style="width:18%" |Wednesday, June 20
!style="width:18%" |Thursday, June 21
!style="width:18%" |Friday, June 22
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''9am-10am:''' What's new in Slicer4 (Group. Multivolumes, Charts.) <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
<br>----------------------------------------<br>
'''10-11am''' Slicer4 Python <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
<br>----------------------------------------<br>
'''11-12pm: <font color="#4020ff">Breakout Session:'''</font> <br>
[[MIT_Project_Week_Rooms#Star|Star Room]]
|'''9am-11pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2012 Project Week Breakout Session: SimpleITK|Slicer and SimpleITK]] (Hans)
[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
<br>----------------------------------------<br>
'''10am-12pm: <font color="#4020ff">Computation Core PIs: closed meeting with Ron:'''</font><br>
[[MIT_Project_Week_Rooms#Star|Star Room]]
|'''9am-4pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2012 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
<br>----------------------------------------<br>
'''10:30am-12pm: <font color="#4020ff">Breakout Session:'''</font><br>
[[MIT_Project_Week_Rooms#Star|Star Room]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-4:30pm''' Slicer4 Extensions (JC) <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]
|'''3-4pm:''' [[2012_Tutorial_Contest|Tutorial Contest Presentations]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''4-5pm:''' Breakout Session: DICOM, Networking, RT, Segmentations (Steve, Greg, Andras, Andre)
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''12:45-1pm:''' [[Events:TutorialContestJune2012|Tutorial Contest Winner Announcement]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3-30pm: <font color="#4020ff">Breakout Session:'''</font>Qt Testing (JC)
|'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> Ultrasound (Tamas)
[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

==Projects==

This is where the list of projects goes...

Please use [http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template THIS TEMPLATE] to create project pages for this event.

==='''Neurosurgery, Brain and Spine, Traumatic Brain Injury'''===

# [[2012_Summer_Project_Week:Early_Dementia_Diagnostic |Early Dementia Diagnostic Tools]] (Marcel Koek, Sonia Pujol)
# Intraoperative White Matter Tract Detection Module (Lauren O'Donnell, Isaiah Norton)
# [[Semiautomatic longitudinal segmentation of MR volumes in traumatic brain injury]] (Andrei Irimia, Danielle Pace, Micah Chambers, Stephen Aylward)
# [[2012_Summer_Project_Week:Radnostics |Spine Segmentation & Osteoporosis Detection In CT Imaging Studies]] (Anthony Blumfield)
# [[2012_Summer_Project_Week:4D_Segmentation_TBI|4D Segmentation of longitudinal MRI of TBI patients]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig)
# An Intraoperative Transcranial Ultrasound Brain Shift Monitor (Jason White, Alex Golby, Isaiah Norton)

==='''Radiation Therapy'''===

#Dose Calculation for Interstitial Brachytherapy (Tina Kapur, Greg Sharp)
#[[2012_Summer_Project_Week:Overlapping_structures|Overlapping structures]] (Greg Sharp, Steve Pieper)
#[[2012_Summer_Project_Week:Atlas_based_segmentation_for_head_and_neck|Atlas-based segmentation for head and neck]] (Greg Sharp, Nadya Shusharina, James Shackleford, Polina Golland)
#[[2012_Summer_Project_Week:SlicerRT|Radiotherapy extensions for Slicer 4]] (Andras Lasso, Csaba Pinter, Kevin Wang)
#[[2012_Summer_Project_Week:Deformable_Registration_for_Head_and_Neck| Deformable Registration for Head and Neck ]] (Ivan Kolesov, Greg Sharp, Yi Gao, Allen Tannenbaum)

==='''Huntington's Disease'''===
# [[2012_Summer_Project_Week:DTIPrep|DTIPrep]] (David Welch)
# [[2012_Summer_Project_Week:Fast Fiducial Registration|Fast Fiducial Registration Module]] (David Welch)
# [[2012_Summer_Project_Week:ANTS Registation|ANTS Registation Module]] (David Welch)
# [[2012_Summer_Project_Week:Nipype Integration|Slicer/Nipype Integration]] (Hans Johnson)
# [[2012_Summer_Project_Week:DicomToNrrd|DicomToNrrdConverter Integration]] (Kent Williams)
# [[2012_Summer_Project_Week:4D shape analysis|4D shape analysis]] (James Fishbaugh, Marcel Prastawa, Guido Gerig)
# [[2012_Summer_Project_Week:DTI-Reg|DTI atlas based fiber analysis]] (Francois Budin)

==='''Atrial Fibrillation'''===
# Model-based segmentation of left Atrium using Graph-cuts (Gopal Veni, Ross Whitaker)
# [[DBP3:Utah:SlicerModuleCardiacRegistration|Cardiac MRI Registration Module]] (Alan Morris, Danny Perry, Josh Cates, Greg Gardner, Rob MacLeod)
# [[DBP3:Utah:VecReg|Vector-Valued Cardiac MRI Registration]] (Yi Gao, Josh Cates, Liang-Jia Zhu, Alan Morris, Danny Perry, Greg Gardner, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
# [[DBP3:Utah:SlicerModuleAutoScar|Automatic Left Atrial Scar Detection]] (Danny Perry, Alan Morris, Josh Cates, Rob MacLeod)
# [[DBP3:Utah:SlicerModuleInhomogeneity|MRI Inhomogeneity Correction Filter]] (Alan Morris, Eugene Kholmovski, Josh Cates, Danny Perry, Rob MacLeod)
# OpenIGT for realtime MRI-guided RF ablation (Rob MacLeod, Junichi Tokuda)

==='''Device Integration with Slicer and General Image Guided Therapy'''===
# [[2012_Summer_Project_Week:iGyne|iGyne for Gyne Brachytherapy]] (Xiaojun Chen, Jan Egger, Tina Kapur, Steve Pieper)
# [[2012_Summer_Project_Week:Open_source_electromagnetic_trackers_using OpenIGTLink|Open-source electromagnetic trackers using OpenIGTLink]] (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)
# [[2012_Summer_Project_Week:LiveUltrasound|Live Ultrasound]] (Tamas Ungi, Andinet Enquobahrie, Junichi Tokuda)
# [[2012_Summer_Project_Week:TransformRecorder|Transform Recorder]] (Simrin Nagpal, Tamas Ungi)
# [[2012_Summer_Project_Week:VertebraCTUSReg|Single Vertebra CT-US Registration]] (Samira Sojoudi, Saman Nouranian, Simrin Nagpal, Tamas Ungi, David Welch)
# [[2012_Summer_Project_Week:ProstateBxReviewWorkflow_Slicer4|Prostate biopsy multiparametric MRI review using Slicer4]] (Andrey Fedorov, Steve Pieper)

==='''General Segmentation'''===
#[[2012_Summer_Project_Week:SemiAutomatedAirwaySegmentationfrom0.64mmLungCTDatasets|Semi-automated airway segmentation from 0.64mm lung CT datasets]] (Padraig Cantillon-Murphy, Raul San Jose Estepar, Pietro Nardelli)
# [[2012_Summer_Project_Week:QuantitativePETImageAnalysisModule|Quantitative PET Image Analysis Module]] (Markus Van Tol)
#Segmentation with Label Fusion (Ramesh Sridharan, Christian Wachinger, Polina Golland)
#[[Loading and segmentation of histopathology imaging for radiological-pathological correlation]] (Tobias Penzkofer)

==='''General Registration'''===
# Interactive registration (Kunlin Cao GRC, Guillaume Pernelle BWH, Simrin Nagpal Queens)
# [[2012_Summer_Project_Week:NiftyReg|NiftyReg integration]] (Marc Modat, Sonia Pujol)
# [[2012_Summer_Project_Week:ElastixIntegration| Elastix integration]] (Stefan Klein, Sonia Pujol)
# [[2012_Summer_Project_Week:DTIRegistration| Highly Deformable DTI Registration for cases with large pathological variations]] (Aditya Gupta, Martin Styner, Matthew Toews)
# [[2012_Summer_Project_Week:ElastixIntegration| Elastix integration]] (Stefan Klein, Sonia Pujol)
# [[2012_Summer_Project_Week:DifficultRegistration| Registration of Difficult Images]] (Matthew Toews, Stefan Klein, Marc Modat, Aditya Gupta, Martin Styner, William Wells)

==='''General Diffusion Tractography'''===
#
#

==='''Vessels'''===
#
#

==='''Informatics'''===
# [[2012_Summer_Project_Week:AIM_for_QIN|Applicability of AIM to QIN use cases]] (Andrey Fedorov, Reinhard Beichel, Jayashree Kalpathy-Cramer, Pat Mongkolwat, Daniel Rubin)

==='''Infrastructure'''===

# [[2012_Summer_Project_Week:SelfTesting|Built-In Self-Testing (BIST) for Slicer]] (Steve, Julien, Jc, Sonia)
# [[2012_Summer_Project_Week:AnnotationModule|Annotation module redesign for Slicer]] (Nicole)
# Multivolume, nrrd, .... (Andriy, Jim)
# Python CLI modules (Demian, JC, Julien). See [http://www.na-mic.org/Bug/view.php?id=2039 #2039]
# [[2012_Summer_Project_Week:Charting|Charting]] (Jim)
# [[2012_Summer_Project_Week:SimpleITK Integration|SimpleITK Integration]] (Hans Johnson, Bradley Lowekamp)
# GPU Editor Effects
# XTK/WebGL Exporter (Daniel, Nicolas - Children's Hospital Boston)
# General Usability issues (e.g. LM,FG,BG blending)
# Callback/Events/Observation best practice + Performance bottleneck discussion (Julien, Steve,...)
# XNAT/Slicer implementation (Sunil, Dan, Steve,...)
# Pilot QIN use cases for Slicer/XNAT integration (Sunil, Steve, Dan, Andriy, Jayashree,...)
# [[2012_Summer_Project_Week:ITKv4 Integration|ITKv4 Integration]] (Hans Johnson, Julien Finet, Jim). See [http://www.na-mic.org/Bug/view.php?id=2007 #2007]
# [[2012_Summer_Project_Week:Reporting|Reporting]] (Andrey)
# [[2012_Summer_Project_Week:LongitudinalPETCTModule|Slicer Module for longitudinal analysis of PET-CT]] (Paul, Andriy, Ron, Markus,...)

==Background==

We are pleased to announce the 15th PROJECT WEEK of hands-on research and development activity for applications in Neuroscience, Image-Guided Therapy and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants. If you would like to learn more about this event, please [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week click here to join our mailing list].

Active preparation begins on Thursday, April 26th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 40-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], [http://www.cimit.org CIMIT], and OCAIRO. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].

== Logistics ==
*'''Dates:''' June 18-22, 2012.
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''REGISTRATION:''' Please click [https://www.regonline.com/namic2012summerprojweek HERE] to do an on-line registration for the meeting that will allow you to pay by credit card. No checks will be accepted.
*'''Registration Fee:''' $300 (covers the cost of breakfast, lunch and coffee breaks for the week).
*'''Hotel:''' No room blocks have been reserved in any area hotel. Please select a [http://web.mit.edu/institute-events/visitor/stay.html |hotel of your choice] and make reservations as early as possible. Some area hotels are:
**marriott cambridge center
**marriott residence inn kendall square
**le meridien central square
**hotel marlowe cambridge
**royal sonesta hotel cambridge

== Preparation ==
# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 26, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on Thursday May 10, all participants to add a one line title of their project to #Projects
# By 3pm ET on Thursday June 7, all project leads to complete [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 14: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Matt)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Where possible, setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Matt)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## See the [http://www.slicer.org/slicerWiki/index.php/Documentation/4.0/Developers Developer Section of slicer.org] for information.
## Projects to develop extension modules should be built against the latest Slicer4 trunk.

==Registrants==

Do not add your name to this list- it is maintained by the organizers based on your paid registration. ([http://www.regonline.com/Register/Checkin.aspx?EventID=1089602 Please click here to register.])

#Anderson, Peter, retired, traneus@verizon.net
#Arbisser, Amelia, MIT, arbisser@mit.edu
#Aucoin, Nicole, BWH, Nicole@bwh.harvard.edu
#Blumfield, Anthony, Radnostics, Anthony.Blumfield@Radnostics.com
#Budin, Francis, NIRAL-UNC, fbudin@unc.edu
#Chauvin, Laurent, SPL, lchauvin@bwh.harvard.edu
#Datar, Manasi, Utah SCI, brenda@sci.utah.edu
#Diedrich, Karl, AZE R&D, karl.diedrich@azeresearch.com
#Egger, Jan, BWH, egger@bwh.harvard.edu
#Fedorov, Andriy, BWH, fedorov@bwh.harvard.edu
#Gouaillard, Alexandre, A*STAR, agouaillard@gmail.com
#Johnson, Hans, Univ Iowa, hans-johnson@uiowa.edu
#Kikinis, Ron, HMS, kikinis@bwh.harvard.edu
#Klein, Stefan, Erasmus MC, s.klein@erasmusmc.nl
#Koek, Marcel, Erasmus MC, m.koek@erasmusmc.nl
#Kumar, Sunil, Washington Univ St Louis, kumars@mir.wustl.edu
#Lasso, Andras, Queen's Univ, lasso@cs.queensu.ca
#Macule, Raul, AZE R&D, raul.macule@azeresearch.com
#Miller, Jim, GE Research, millerjv@ge.com
#Modat, Marc, Univ College London, m.modat@ucl.ac.uk
#Moloney, Brendan, AIRC, moloney.brendan@gmail.com
#Mongkolwat, Pattanasak, Northwestern U, p-mongkolwat@northwestern.edu
#Nagpal, Simrin, Queen’s Univ, 7sn6@cs.queensu.ca
#Nardelli, Pietro, Univ College Cork, pie.nardelli@gmal.com
#Paniagua, Beatriz, Univ NC Chapel Hill, bpaniagua@gmail.com
#Pieper, Steve, Isomics, pieper@bwh.harvard.edu
#Pinter, Csaba, Queen's Univ, pinter@cs.queensu.ca
#Pujol, Sonia, BWH, spujol@bwh.harvard.edu
#Ungi, Tamas, Queen's Univ, ungi@cs.queensu.ca
#Van Tol, Markus, Univ Iowa, mvantol@engineering.uiowa.edu
#Welch, David, Univ Iowa, david-welch@uiowa.edu
#Yarmakovich, Alex, Isomics, alexy@bwh.harvard.edu

2012 Project Week:RemoveSlicerLegacyCode

2012-01-09T20:15:29Z

Hjmjohnson: Created page with '__NOTOC__ <gallery> Image:PW-SLC2011.png|Projects List </gallery> ==Key Investigators== * Iowa: Hans Johnson * Kitware: Jean-Christophe Fil…'

__NOTOC__
<gallery>
Image:PW-SLC2011.png|[[2012_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Iowa: Hans Johnson
* Kitware: Jean-Christophe Fillion-Robin, Julien Finet
* Isomics: Steve Pieper
* GE: Jim Miller
<div style="margin: 20px;">

Slicer has many modules that have had subsequent better methods developed. In many cases the old modules are recommended to NOT use them, so they should be removed, or at least hidden from view.

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
Identify where the old tools should go.</div>

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Discussion and identify work duties
</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

2012 Winter Project Week

2012-01-09T20:11:23Z

Hjmjohnson: /* NA-MIC Kit Internals */

Back to [[Project Events]], [[Events]]
Back to [[Project Events]], [[AHM_2012]], [[Events]]

__NOTOC__
[[image:PW-SLC2012.png|300px]]

== Dates.Venue.Registration ==

Please [[AHM_2012#Dates_Venue_Registration|click here for Dates, Venue, and Registration]] for this event.

== [[AHM_2012#Agenda|'''AGENDA''']] and Project List==

Please:
* [[AHM_2012#Agenda|'''Click here for the agenda for AHM 2012 and Project Week''']].
* [[#Projects|'''Click here to jump to Project list''']]

==Background==

From January 9-13, 2012, the 14th project week for hands-on research and development activity in Neuroscience and Image-Guided Therapy applications will be hosted in Salt Lake City, Utah. Participant engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithms, medical imaging sequence development, tracking experiments, and clinical applications. The main goal of this event is to further the translational research deliverables of the sponsoring centers ([http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]) and their collaborators by identifying and solving programming problems during planned and ad hoc break-out sessions.

Active preparation for this conference begins with a kick-off teleconference. Invitations to this call are sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties expressing an interest in working with these centers. The main goal of the initial teleconference is to gather information about which groups/projects would be active at the upcoming event to ensure that there were sufficient resources available to meet everyone's needs. Focused discussions about individual projects are conducted during several subsequent teleconferences and permits the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in break-out sessions. In the final days leading up to the meeting, all project teams are asked to complete a template page on the wiki describing the objectives and research plan for each project.

On the first day of the conference, each project team leader delivers a short presentation to introduce their topic and individual members of their team. These brief presentations serve to both familiarize other teams doing similar work about common problems or practical solutions, and to identify potential subsets of individuals who might benefit from collaborative work. For the remainder of the conference, about 50% time is devoted to break-out discussions on topics of common interest to particular subsets and 50% to hands-on project work. For hands-on project work, attendees are organized into 30-50 small teams comprised of 2-4 individuals with a mix of multi-disciplinary expertise. To facilitate this work, a large room is setup with ample work tables, internet connection, and power access. This enables each computer software development-based team to gather on a table with their individual laptops, connect to the internet, download their software and data, and work on specific projects. On the final day of the event, each project team summarizes their accomplishments in a closing presentation.

A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].

==Projects==

===Traumatic Brain Injury ===

* [[2012_Winter_Project_Week:TBIClinicalAnalysis|Segmentation of Serial MRI of TBI patients
using Personalized Atlas Construction]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIDTIAnalysis|Registration and analysis of white matter tract changes in TBI]] (Clement Vachet, Anuja Sharma, Marcel Prastawa, Andrei Irimia, Jack van Horn, Guido Gerig, Martin Styner, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIValidation|Validation, visualization and analysis of segmentation for TBI]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:GeometricMetamorphosisTBI|Geometric Metamorphosis for TBI]] (Danielle Pace, Marc Niethammer, Marcel Prastawa, Andrei Irimia, Jack van Horn, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIRegistration|Multimodal Deformable Registration of Traumatic Brain Injury MR Volumes using Graphics Processing Units]] (Yifei Lou, Andrei Irimia, Patricio Vela, Allen Tannenbaum, Micah C. Chambers, Jack Van Horn and Paul M. Vespa, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIRegistration|Integration of unscented Kalman filter (UKF) based multi-tensor tractography in Slicer]] (Christian Baumgartner, Yogesh Rathi, Carl-Fredrik Westin)

===Predict Huntington's Disease===
* [[2012_Winter_Project_Week:SPIEWorkshop|SPIE DTI Workshop Preparation: Perform DTI Quality Control]] (Jean-Baptiste Berger, Sonia Pujol, Guido Gerig, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:DWIPhantom|DTI tractography phantom: a software for evaluating tractography algorithms]] (Gwendoline Roger,Yundi Shi, Clement Vachet, Martin Styner, Sylvain Gouttard)
* [[2012_Winter_Project_Week:FVLight|FiberViewerLight: a fiber bundle visualization and clustering tool]] (Jean-Baptiste Berger, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:DTIAFA|DTIAtlasFiberAnalyzer]] (Jean-Baptiste Berger, Yundi Shi, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:PairWiseDTIRegistration|Pairwise DTI registration: DTI-Reg]] (Clement Vachet, Hans Johnson, Martin Styner)
* [[2012_Winter_Project_Week:ShapeAnalysisSubcorticalStructuresHD|Morphometric analysis in subcortical structures in HD]] (Beatriz Paniagua, Clement Vachet, Hans Johnson, Martin Styner)
* [[2012_Winter_Project_Week:DTI pipeline|Applying our DTI pipeline to analyse HD data]] (Gopalkrishna Veni, Hans Johnson, Martin Styner, Ross Whitaker)
* [[2012_Winter_Project_Week: DTI Change Modeling | Longitudinal change modeling of fiber tracts in serial HD DTI data]] (Anuja Sharma, Hans Johnson, Guido Gerig)
* [[2012_Winter_Project_Week: Continuous 4D shapes | Continuous 4d shape models from time-discrete data: Subcortical structures in HD]] (James Fishbaugh, Hans Johnson, Guido Gerig)

===Atrial fibrillation ===
* [[2012_Winter_Project_Week:EndoSeg|Endocardial Segmentation in DE-MRI for AFib]] (Yi Gao, Liang-Jia Zhu, Josh Cates, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:LAWallRegistration|Longitudinal Alignment and Visualization of Left-Atrial Wall from DEMRI and MRA]] (Josh Cates, Yi Gao, Liang-Jia Zhu, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:PVRegistration|Longitudinal Alignment and Visualization of Pulmonary Veins from DEMRI and MRA]] (Josh Cates, Yi Gao, Liang-Jia Zhu, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:RealTime|OpenIGT for realtime MRI-guided RF ablation]] (Gene Payne, Rob MacLeod, and Junichi Tokuda)
* [[2012_Winter_Project_Week:GraphbasedSeg|Graph based segmentation on LGE-MRI data]] (Gopal Veni, Ross Whitaker)

===Head and Neck Cancer ===
* [[2012_Winter_Project_Week:PatchBased|A patch-based approach to the segmentation of organs of risk]] (Christian Wachinger, Polina Golland)
* [[2012_Winter_Project_Week:PairwiseLF|Label fusion with pairwise interactions]] (Ramesh Sridharan, Christian Wachinger, Polina Golland)
* [[RT dose comparison tool for Slicer]] (Nadya Shusharina, Greg Sharp)
* [[2012_Winter_Project_Week:InteractiveSegmentation|Interactive editing tools for segmentation]] (Greg Sharp, Steve Pieper)
* [[2012_Winter_Project_Week:UserInTheLoop_InteractiveSegmn|Interactive 3D Level-Set Segmentation]] (Peter Karasev, Karl Fritscher, Ivan Kolesov, Allen Tannenbaum)
*[[2012_Winter_Project_Week:GBMseg|Segmentation of polymodal images of GBM's in Slicer]] (Misha Milchenko, Dan Marcus, Andrey Fedorov, Jan Egger, Isaiah Norton, Jayashree)

===IGT for Surgery and Radiation Treatments===
*[[2012_Winter_Project_Week:OpenIGTLink_Interface_for_Slicer4| OpenIGTLink interface for Slicer4]] (Junichi Tokuda, Clif Burdette/Jack Blevins, Tamas Ungi, Andras Lasso)
*[[2012_Winter_Project_Week:LiveUltrasound|Live ultrasound in Slicer4 using Plus and OpenIGTLink]] (Tamas Ungi, Elvis Chen)
*[[2012_Winter_Project_Week:4DUltrasound|4D Ultrasound Storage and Volume Rendering on Slicer 3.6]] (Laurent, Noby)
*[[2012_Winter_Project_Week:BKPLUSSlicer|Integration of BK Ultrasound into PLUS and Slicer]] (Mehdi Moradi, Isaiah Norton, Tamas Ungi)
*[[2012_Winter_Project_Week:PelvicRegistration|Deformable prostate registration: 3D ultrasound to MRI]] (Mehdi Moradi, Jan Egger, Andrey Fedorov)
*[[2012_Winter_Project_Week:iGyne | iGyne: A Software Prototype to support Gynecologic Radiation Treatment in AMIGO]] (Jan Egger, Xiaojun Chen, Radhika Tibrewal, Mehdi Moradi, Antonio Damato, Kanokpis Townamchai, Tina Kapur, Akila Viswanathan)
*[[2012_Winter_Project_Week:Needle Detection in MR Images for Brachytherapy in AMIGO|Needle Detection in MR Images for Brachytherapy in AMIGO]] (Radhika Tibrewal, Jan Egger, Xiaojun Chen, Matthew Toews, Stephen Aylward)
*[[2012_Winter_Project_Week:hybridMRS | Generation of a hybrid MR-Spectroscopic (MRS) dataset under 3DSlicer for Neurosurgery]] (Jan Egger, Isaiah Norton, Bjoern Menze, Daniel Hořínek, Antonín Škoch, Jens Sommer, Christopher Nimsky, Alexandra Golby, Tina Kapur)
*[[2012_Winter_Project_Week:RTTools|RT tools for Slicer4]] (Csaba Pinter, Kevin Wang, Andras Lasso, Greg Sharp)
*[[2012_Winter_Project_Week:RTSS|RT structure set data representation]] (Greg Sharp, Andras Lasso, Steve Pieper, etc.)

===Musculoskeletal System===
* [[2012_Winter_Project_Week:Radnostics|Spine Segmentation & Osteoporosis Screening In CT Imaging Studies]] (Anthony Blumfield)

===Registration===
* [[2012_Winter_Project_Week:CMFreg|Framework for Cranio-Maxillo Facial registration in Slicer3]] (Beatriz Paniagua, Lucia Cevidanes, Martin Styner)
* [[2012_Winter_Project_Week:SlidingOrgans|Registration in the presence of sliding between organs (Danielle Pace, Marc Neithammer, Stephen Aylward)]]
* [[2012_Winter_Project_Week:GeometricMetamorphosis|Estimating the infiltration / recession of pathologies independent of background deformations (Danielle Pace, Stephen Aylward, Marc Niethammer)]]
* [[2012_Winter_Project_Week:FastInterpolation|Fast Image Interpolation Given Parameterized Deformations For Image Registration (Ivan Kolesov, Greg Sharp, Allen Tannenbaum)]]
* [[2012_Winter_Project_Week:CTLiverRegistration|Register liver CT images for tumor progress monitoring]] (Karl Diedrich, Nobuhiko Hata, Atsushi Yamada)

===Shape Analysis===
* [[2012_Winter_Project_Week:PNSnormals|Principal Nested Spheres Normal Consistency in ShapeWorks]] (Beatriz Paniagua, Josh Cates, Manasi Datar, Ross Whitaker, Martin Styner)
* [[2012_Winter_Project_Week:GeomIndicesSlicer4|Porting of White Matter Geometric Indices Module to Slicer4]] (Peter Savadjiev)
* [[2012_Winter_Project_Week:ParticleWrapper|Slicer end-to-end particle correspondence wrapper module]] (Ipek Oguz, Beatriz Paniagua, Josh Cates, Manasi Datar, Ross Whitaker, Martin Styner)

===NA-MIC Kit Internals===
*Slicer4 release (Jean-Christophe Fillion-Robin (JC), and Julien Finet (J2))
*Slicer4 extensions (JC)
*Slicer4 documentation (JC)
*Slicer4 GUI Testing (Benjamin Long, JC, J2)
*Slicer4 data on MIDAS (Josh Cates, Patrick Reynolds)
*[[2012_Project_Week:SceneViews|Slicer4 Scene Views Module]] (Nicole Aucoin, Ron Kikinis, Julien Finet)
*[[2012_Project_Week:AnnotationsFileFormatRefactor|Annotations Module File Format Refactor]] (Nicole Aucoin)
*[[2012_Project_Week:QT3DTextRendering|QT 3D Text rendering proof of concept]] (Julien Finet, Steve Pieper, Nicole Aucoin)
*[[2012_Project_Week:DICOM|DICOM Networking, Database, and Slicer Integration]] (Steve, Andrey, Andras)
*[[2012_Project_Week:EditorExtensions|Editor Extension Examples and Debugging]] (Steve, Andrey, Jc, Hans, Satra)
*[[2012_Project_Week:GeneralGUI|General minor GUI redesign]] (Wendy Plezniak, Julien Finet, Ron Kikinis)
*[[2012_Project_Week:ViewerControls|Redesign of the slice viewer control panels]] (Julien Finet, Ron Kikinis, Hans Johnson, Greg Sharp)
*[[2012_Project_Week:AutomatedTesting |Automated Testing (Sonia Pujol, Steve Pieper, Jc, Benjamin)]]
*[[2012_Project_Week:RemoveSlicerLegacyCode|Remove legacy code from slicer4 (itk, modules, build scripts) (Hans, Jim, Steve, J2, JC)]]
*[[2012_Project_Week:BatchProcessing|Batch Processing with Slicer Modules]] (Steve, Andrey, JC, Hans, Satra)
*[[2012_Project_Week:4DImageSlicer4|Support for 4D Images in Slicer4]] (Andrey, Steve, Junichi, Alex)
*[[2012_Project_Week:QIN-SAM|QIN Slicer Annotation Module: AIM, DICOM SR and Slicer annotations]] (Andrey, Steve, Nicole, Jayashree)

=== Preparation ===

#Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]
#Starting Thursday, October 27th, part of the weekly Thursday 3pm NA-MIC Engineering TCON will be used to prepare for this meeting. The schedule for these preparatory calls is as follows:
#*October 27: MGH DBP
#*November 3: Iowa DBP Huntingtons, Engineering Infrastructure Topics
#*November 10: Utah Atrial Fibrillation DBP
#*November 17: UCLA TBI DBP
#*November 24: No call. thanksgiving.
#*December 1:
#*December 8:
#*December 15:Finalize Projects
#*January 5: Loose Ends
#By December 15: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
#By December 15: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]
##Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
##Gather test images in any of the Data sharing resources we have (e.g. MIDAS, xNAT). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
##Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
#Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

2012 Winter Project Week DBP Iowa Team Meeting

2012-01-09T17:16:42Z

Hjmjohnson:

[[AHM_2012#Agenda|Back to AHM Schedule]]

This session is for the agenda for the Iowa DBP team meeting with Ron.

# DBP Data and its use by Core 1
# DTI Workflow in Slicer
# Longitudinal DTI analysis of HD data
# Longitudinal Shape analysis of HD data
## [Continuous 4D shapes|http://www.na-mic.org/Wiki/index.php/2012_Winter_Project_Week:_Continuous_4D_shapes]

2011 Slicer4-PreRSNAHackFest

2011-11-02T10:09:55Z

Hjmjohnson: /* Participants */

=What=
Slicer 4 PreRSNA Sprint.

Since neither mantis or a high-level phone call really captures the kinds of issues we are currently facing.
The core developers need to be looking at the code and errors together to understand issues and implement the appropriate solutions.

=Who=
Core developers

=Where=
Google hangouts with extra - https://plus.google.com/hangouts/extras/talk.google.com/slicer

=When=
November 3rd, starting at 1pm CST. See [http://www.worldtimeserver.com/convert_time_in_US-IA.aspx?y=2011&mo=11&d=3&h=13&mn=0 TimeZone converter]

=Participants=


{|class="wikitable alternance" style="text-align:left; width:100%; border:1px solid black;"
|+ '''''Participants'''''
|-
! scope=col style="background:#cde6f8;"| Name
! scope=col style="background:#cde6f8;"| Available Operating System
! scope=col style="background:#cde6f8;"| Remarks
|-
| Nicole Aucoin
| {{Not Done}}
|
|-
| Jean-Christophe Fillion-Robin
| Workstation(s): [[Image:Os_linux_small.png]] Ubuntu 10.04, ''Slow'' remote access: [[Image:Os_win_small.png]] Windows7 (VS2008 32bits, VS2008 64bits), [[Image:Os_macosx_small.png]] MacOSX 10.?
|
|-
| Julien Finet
| {{Not Done}}
|
|-
| Hans Johnson
| {{Not Done}}
|
|-
| Jim Miller
| Mac 64bit 10.6.8
|
|-
| Steve Pieper
| {{Not Done}}
|
|-
| Kilian Pohl
| {{Not Done}}
|
|}

=Issues=
{{note}}''Describe the issue shortly and add the corresponding mantis link.''

{|class="wikitable alternance" style="text-align:left; width:100%; border:1px solid black;"
|+ '''''Issues'''''
|-
! scope=col style="background:#cde6f8;"| Progress
! scope=col style="background:#cde6f8;"| Issue#
! scope=col style="background:#cde6f8;"| Developer
! scope=col style="background:#cde6f8;"| Short description / Notes
|-
| {{Not Done}} 
| [http://na-mic.org/Mantis/view.php?id=1375 1375]
| Jc
| QT_PLUGIN_PATH not set right on windows install
|-
| {{Not Done}}
| [http://na-mic.org/Mantis/view.php?id=1464 1464]
| Jc
| Slicer crash while trying to call CLI module from python
|}

2011 Summer Project Week Iowa Huntington's disease data sharing

2011-06-22T21:28:24Z

Hjmjohnson: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
</gallery>

'''Full Title of Project'''

==Key Investigators==
* UIowa: Hans Johson, Mark Scully

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
Share a subset of the Huntington's disease data from UIowa.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
Data will be made available via xnat.

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
Data is shared as the NAMIC_HD project on xnat at https://predict-hd.net/xnat.

Fill out the form [[File:NAMIC_DATA_SHARING.doc]] to request access.

After access has been granted and an account has been created the script [[File:Fetch_NAMIC_HD_data.sh.gz]] will help you download the data.

</div>
</div>

<div style="width: 97%; float: left;">

==References==

==Delivery Mechanism==



This work will be delivered to the NAMIC Kit as a project in the xnat instance at https://predict-hd.net/xnat

2011 Summer Project Week BRAINSFit new features integration

2011-06-19T17:31:26Z

Hjmjohnson: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
Image:notfound.png|Interesting picture to be added...
</gallery>

'''Full Title of Project'''

==Key Investigators==
* BWH: Andrey Fedorov
* U.Iowa: Hans Johnson, Mark Scully

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>

* Discuss and integrate some new features into BRAINSFit registration module
* Review http://review.source.kitware.com/#change,1856
** determine how this effort overlaps with ITKv4 BSpline work by Nick Tustison
** determine how meta-information will be stored to properly interpret the transform files

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>

* Several registration optimizations have been implemented in a specialized module derived from BRAINSFit, which turned out to be very useful in certain registration scenarios:
** registration initialization using centers of gravity of the mask ROIs
** initialization of the B-spline control point grid to span the bounding box of the ROI instead of the whole image ROI
* We plan to discuss the integration of these features into the mainstream BRAINSFit distribution with the core BRAINSFit developers, and work on the actual integration and development of automated tests for these new features

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>



</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==



This work will be delivered to the NAMIC Kit as a

* Slicer command line module

2011 Summer Project Week

2011-06-02T20:09:46Z

Hjmjohnson: /* Projects */

Back to [[Events]]

[[image:PW-MIT2011.png|right|200px]]

*'''Dates:''' June 20-24, 2011
*'''Location:''' MIT

==Preliminary Agenda==
==Agenda==

{|border="1"
|-style="background: #b0d5e6; color: #02186f; font-size: 130%"
!Time
!width="250px"|Monday, June 20
!width="250px"|Tuesday, June 21
!width="250px"|Wednesday, June 22
!width="250px"|Thursday, June 23
!width="250px"|Friday, June 24
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''9am-11am:''' [[2011 Project Week Breakout Session: Slicer4|Slicer 4 Core Modules Usability Review]]''' [[MIT_Project_Week_Rooms#Star|Star Room]]
<br>----------------------------------------<br>
'''11-12pm: <font color="#4020ff">Breakout Session:'''</font> [[2011 Summer Project Week Breakout Session Slicer4 Annotation|Slicer4 Annotations]] (Nicole Aucoin)<br>
[[MIT_Project_Week_Rooms#Star|Star Room]]
|'''9am-12pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2011 Project Week Breakout Session: ITK|ITK]] (Luis Ibanez)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''9am-5pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2011 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-5:00pm: NA-MIC Kit Update''' (Aylward, Miller, Pieper)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:MultiVolumeContainer#Summer_2011_Project_Week_Breakout_Session Slicer4 MultiVolume Containers] (Nicole Aucoin)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
<br>----------------------------------------<br>
'''3-4pm:''' [[Summer_2011_Tutorial_Contest|Tutorial Contest Presentations]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''4-5pm:''' [[2011 Summer Project Week Breakout Session VTKCharts|VTK Charts]] (Marcus Hanwell)
<br>[[MIT_Project_Week_Rooms#32-D407|32-D407]]
<br>----------------------------------------<br>
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''12:45-1pm:''' [[Events:TutorialContestJune2011|Tutorial Contest Winner Announcement]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3-4pm: <font color="#4020ff">Breakout Session:'''</font><br>Inter-subject Registration for EM segmenter
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
<br>----------------------------------------<br>
<br>'''5pm: <font color="#4020ff">Reception'''</font><br>
<br>[[MIT_Project_Week_Rooms#R&D Pub|R&D Pub]]
|'''1-2pm: <font color="#4020ff">Breakout Session:'''</font><br> TBD
<br>----------------------------------------<br>
'''2-3pm:'''Breakout Session:TBD'''
<br>----------------------------------------<br>
'''3-4pm: <font color="#4020ff">Breakout Session: TBD'''</font><br>
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

==Projects==
#valuate the applicability of DICOM RT I/O facility in Slicer (via Plastimatch Extension) for Brachytherapy Planning (Tina Kapur, Greg Sharp, Robert Cormack?)
#Visualization of b-spline and vector fields (Steve, Danielle, Dominik)
#Annotation Module in Slicer4 (Nicole Aucoin, Daniel Haehn)
#Slicer4 Multivolume Containers (Ron Kikinis, Nicole Aucoin, Steve Pieper, ... )
#RECIST Slicer4 module (Nicole Aucoin)
#DicomToNrrdConverter refactoring ( Xiaodong Tao, Mark Scully)
#UNC Antialiasing Software as a Slicer extension or ITK module (Steve Pizer, Brad Davis, Petter Risholm, Andriy Fedorov)
# Normal consistency in particle correspondence computation using great circles in principal spheres - Huntington's Disease (Beatriz Paniagua, Martin Styner, Sungkyu Jung, Marc Scully)
# Group-wise Automatic Mesh-Based analysis of CortIcal Thickness (GAMBIT) - TBI (Clement Vachet, Martin Styner, Randi Gollub?)
#[[2011_Summer_Project__Week_Shape_Analysis_UNC |SPHARM & particles shape analysis - Huntington's Disease]] - Lucile Bompard, Clement Vachet, Mark Scully, Beatriz Paniagua, Martin Styner
# Non-rigid, inter-patient registration of bone masks derived from CT for Head and Neck Cancer Radiation Therapy (Ivan Kolesov, Yi Gao, Gregory Sharp, and Allen Tannenbaum)
# Robust Statiistical Segmentation (RSS) for the Atrial Fibrillation Ablation Therapy (Yi Gao, Kedar Patwardhan, Wassim Haddad, and Allen Tannenbaum, Rob MacLeod, Josh Blauer, and Josh Cates)
#Mass Spectrometry for Brain Tumor Therapy (Behnood Gholami, Nathalie Agar)
#Multimodality Image Registration for TBI? (Yifei Lou, Danielle Pace, Jack Van Horn?, Marcel Prastawa?)
# Segmentation of Longitudinal TBI data (Bo Wang, Jack Van Horn, Andrei Irimia, Marcel Prastawa, Guido Gerig)
# Longitudinal Shape Regression - Huntington's Disease (James Fishbaugh, Guido Gerig)
# Dose volume histograms in Slicer (Greg Sharp, Nadya Shusharina, Steve Pieper, Csaba Pinter, Tina Kapur)
# [[2011_Summer_Project__Week_DICOM_RT|Synthetic images, vector fields, RT structures and RT doses in Slicer and ITK]]. (Nadya Shusharina, Greg Sharp, Luis Ibanez, Steve Pieper)
# Interactive Watersheds Segmentation Module for Slicer for Atrial Fibrillation and HN Cancer (Josh Cates, Ross Whitaker, Steve Pieper, Jim Miller, Nadya)
# Segmentation of Nerve and Nerve Ganglia in the Spine (Adrian Dalca, Giovanna Danagoulian, Ron Kikinis, Ehud Schmidt, Polina Golland)
# Image Manifold Learning with Spectral Embedding and Laplacian Eigenmaps (Ramesh Sridharan, Polina Golland)
# Shapeworks Shape Analysis for Atrial Fibrilliation and HD (Manasi Datar, Beatriz UNC, Marc Scully)
#Explore the applicability of RSS and Shapeworks for Ventricular Segmentation(Chiara Carminati, ?, ?)
# Integrate BRAINSCut into Slicer3(Regina Kim, ... )
# The Vascular Modeling Toolkit in 3D Slicer 4 (Daniel Haehn, Luca Antiga, Steve Pieper)
# Integration of LANDWARP into interactive registration module for MR-guided prostate biopsy (Andrey Fedorov, Greg Sharp, Nadya Shusharina)
# Registration of mouse brains (Francois Budin)
# ShapeWorks Applications (Manasi Datar, Beatriz Paniagua, Martin Styner, Ross Whitaker, ?)
# Wireless joystick controlling Slicer4 (Szymon Kostrzewski)
# Live Tracked Ultrasound in 3D Slicer 4 (Tamas Heffter)
# [http://wiki.na-mic.org/Wiki/index.php/Survey_stealthlink_openigtlink Surveying research teams interested in Open IGT Link support of Stealth Station (Nobuhiko Hata, Ron Kikinis)]
# DTIPrep - "Study-specific Protocol" based automatic DWI/DTI quality control and preparation - Huntington's Disease (Mashid Farzinfar, Clement Vachet, Joy Matsui, Martin Styner)
# DTIProcessing - Huntington's Disease (Clement Vachet, Joy Matsui, Martin Styner)
# Volumetric DTI into Slicer for HD for Tract based roi segmentation (Steve Callahan, Marc Scully, Jim Miller)
#Nifti Support for Diffusion Tensor Images (Demian)
# Finishing details on the workflows: DICOM->Full brain tractography / peritumoral (Demian)
# Refactoring of the tractography display widget (Isaiah)
# Laterality (Lauren)
# Selection for models and bundles post-clustering (Lauren)
#ROI-based / picking selection of fiber bundles (Maybe one of Sylvain's interns)
#Adding streamlined tractography to the Finsler front propagation tractography toolkit (Antonio)
#Add ODF estimation / visualization (Antonio)
# Workflows and Service Oriented Architecture Modules for Slicer4 as Extensions (Alexander Zaitsev, Wendy Plesniak, Ron Kikinis)
# [[2011_Summer_Project__Week_DICOM_Networking|DICOM Networking interface for Slicer4]] (Steve Pieper, Nicole Aucoin, Noby Hata)
# Stenosis Detector in 3D Slicer 4 (Suares Tamekue, Daniel Haehn, Luca Antiga)

==Background==

We are pleased to announce the 13th PROJECT WEEK of hands-on research and development activity for applications in Image-Guided Therapy, Neuroscience, and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants. If you would like to learn more about this event, please [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week click here to join our mailing list].

Active preparation begins on Thursday, April 28th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 40-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].

== Logistics ==
*'''Dates:''' June 20-24, 2011
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''REGISTRATION:''' Please register [http://guest.cvent.com/d/sdqy0l/4W here]. Payment must be made by credit card.
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week).
*'''Hotel:''' Boston Marriott Cambridge, Two Cambridge Center, 50 Broadway, Cambridge, MA 02142. Group rate is $199/night plus tax. Book [http://www.marriott.com/hotels/travel/boscb?groupCode=jrbjrba&app=resvlink&fromDate=6/19/11&toDate=6/24/11 here] or call 1-617-494-6600 and mention that you are booking in the MIT Room Block. '''All reservations must be made by May 29, 2011 to receive the discounted rate.'''

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 28, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on Thursday May 12, all participants to add a one line title of their project to #Projects
#By 3pm ET on Thursday June 9, all project leads to complete [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 16: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/#dirlist Slicer-3-6 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

2011 Summer Project Week

2011-06-02T20:09:18Z

Hjmjohnson: /* Projects */

Back to [[Events]]

[[image:PW-MIT2011.png|right|200px]]

*'''Dates:''' June 20-24, 2011
*'''Location:''' MIT

==Preliminary Agenda==
==Agenda==

{|border="1"
|-style="background: #b0d5e6; color: #02186f; font-size: 130%"
!Time
!width="250px"|Monday, June 20
!width="250px"|Tuesday, June 21
!width="250px"|Wednesday, June 22
!width="250px"|Thursday, June 23
!width="250px"|Friday, June 24
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''9am-11am:''' [[2011 Project Week Breakout Session: Slicer4|Slicer 4 Core Modules Usability Review]]''' [[MIT_Project_Week_Rooms#Star|Star Room]]
<br>----------------------------------------<br>
'''11-12pm: <font color="#4020ff">Breakout Session:'''</font> [[2011 Summer Project Week Breakout Session Slicer4 Annotation|Slicer4 Annotations]] (Nicole Aucoin)<br>
[[MIT_Project_Week_Rooms#Star|Star Room]]
|'''9am-12pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2011 Project Week Breakout Session: ITK|ITK]] (Luis Ibanez)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''9am-5pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2011 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-5:00pm: NA-MIC Kit Update''' (Aylward, Miller, Pieper)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:MultiVolumeContainer#Summer_2011_Project_Week_Breakout_Session Slicer4 MultiVolume Containers] (Nicole Aucoin)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
<br>----------------------------------------<br>
'''3-4pm:''' [[Summer_2011_Tutorial_Contest|Tutorial Contest Presentations]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''4-5pm:''' [[2011 Summer Project Week Breakout Session VTKCharts|VTK Charts]] (Marcus Hanwell)
<br>[[MIT_Project_Week_Rooms#32-D407|32-D407]]
<br>----------------------------------------<br>
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''12:45-1pm:''' [[Events:TutorialContestJune2011|Tutorial Contest Winner Announcement]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3-4pm: <font color="#4020ff">Breakout Session:'''</font><br>Inter-subject Registration for EM segmenter
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
<br>----------------------------------------<br>
<br>'''5pm: <font color="#4020ff">Reception'''</font><br>
<br>[[MIT_Project_Week_Rooms#R&D Pub|R&D Pub]]
|'''1-2pm: <font color="#4020ff">Breakout Session:'''</font><br> TBD
<br>----------------------------------------<br>
'''2-3pm:'''Breakout Session:TBD'''
<br>----------------------------------------<br>
'''3-4pm: <font color="#4020ff">Breakout Session: TBD'''</font><br>
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

==Projects==
#valuate the applicability of DICOM RT I/O facility in Slicer (via Plastimatch Extension) for Brachytherapy Planning (Tina Kapur, Greg Sharp, Robert Cormack?)
#Visualization of b-spline and vector fields (Steve, Danielle, Dominik)
#Annotation Module in Slicer4 (Nicole Aucoin, Daniel Haehn)
#Slicer4 Multivolume Containers (Ron Kikinis, Nicole Aucoin, Steve Pieper, ... )
#RECIST Slicer4 module (Nicole Aucoin)
#DicomToNrrdConverter refactoring ( Xiaodong Tao, Mark Scully)
#UNC Antialiasing Software as a Slicer extension or ITK module (Steve Pizer, Brad Davis, Petter Risholm, Andriy Fedorov)
# Normal consistency in particle correspondence computation using great circles in principal spheres - Huntington's Disease (Beatriz Paniagua, Martin Styner, Sungkyu Jung, Marc Scully)
# Group-wise Automatic Mesh-Based analysis of CortIcal Thickness (GAMBIT) - TBI (Clement Vachet, Martin Styner, Randi Gollub?)

#[[2011_Summer_Project__Week_Shape_Analysis_UNC |SPHARM & particles shape analysis - Huntington's Disease]] - Lucile Bompard, Clement Vachet, Mark Scully, Beatriz Paniagua, Martin Styner
# Non-rigid, inter-patient registration of bone masks derived from CT for Head and Neck Cancer Radiation Therapy (Ivan Kolesov, Yi Gao, Gregory Sharp, and Allen Tannenbaum)
# Robust Statiistical Segmentation (RSS) for the Atrial Fibrillation Ablation Therapy (Yi Gao, Kedar Patwardhan, Wassim Haddad, and Allen Tannenbaum, Rob MacLeod, Josh Blauer, and Josh Cates)
#Mass Spectrometry for Brain Tumor Therapy (Behnood Gholami, Nathalie Agar)
#Multimodality Image Registration for TBI? (Yifei Lou, Danielle Pace, Jack Van Horn?, Marcel Prastawa?)
# Segmentation of Longitudinal TBI data (Bo Wang, Jack Van Horn, Andrei Irimia, Marcel Prastawa, Guido Gerig)
# Longitudinal Shape Regression - Huntington's Disease (James Fishbaugh, Guido Gerig)
# Dose volume histograms in Slicer (Greg Sharp, Nadya Shusharina, Steve Pieper, Csaba Pinter, Tina Kapur)
# [[2011_Summer_Project__Week_DICOM_RT|Synthetic images, vector fields, RT structures and RT doses in Slicer and ITK]]. (Nadya Shusharina, Greg Sharp, Luis Ibanez, Steve Pieper)
# Interactive Watersheds Segmentation Module for Slicer for Atrial Fibrillation and HN Cancer (Josh Cates, Ross Whitaker, Steve Pieper, Jim Miller, Nadya)
# Segmentation of Nerve and Nerve Ganglia in the Spine (Adrian Dalca, Giovanna Danagoulian, Ron Kikinis, Ehud Schmidt, Polina Golland)
# Image Manifold Learning with Spectral Embedding and Laplacian Eigenmaps (Ramesh Sridharan, Polina Golland)
# Shapeworks Shape Analysis for Atrial Fibrilliation and HD (Manasi Datar, Beatriz UNC, Marc Scully)
#Explore the applicability of RSS and Shapeworks for Ventricular Segmentation(Chiara Carminati, ?, ?)
# Integrate BRAINSCut into Slicer3(Regina Kim, ... )
# The Vascular Modeling Toolkit in 3D Slicer 4 (Daniel Haehn, Luca Antiga, Steve Pieper)
# Integration of LANDWARP into interactive registration module for MR-guided prostate biopsy (Andrey Fedorov, Greg Sharp, Nadya Shusharina)
# Registration of mouse brains (Francois Budin)
# ShapeWorks Applications (Manasi Datar, Beatriz Paniagua, Martin Styner, Ross Whitaker, ?)
# Wireless joystick controlling Slicer4 (Szymon Kostrzewski)
# Live Tracked Ultrasound in 3D Slicer 4 (Tamas Heffter)
# [http://wiki.na-mic.org/Wiki/index.php/Survey_stealthlink_openigtlink Surveying research teams interested in Open IGT Link support of Stealth Station (Nobuhiko Hata, Ron Kikinis)]
# DTIPrep - "Study-specific Protocol" based automatic DWI/DTI quality control and preparation - Huntington's Disease (Mashid Farzinfar, Clement Vachet, Joy Matsui, Martin Styner)
# DTIProcessing - Huntington's Disease (Clement Vachet, Joy Matsui, Martin Styner)
# Volumetric DTI into Slicer for HD for Tract based roi segmentation (Steve Callahan, Marc Scully, Jim Miller)
#Nifti Support for Diffusion Tensor Images (Demian)
# Finishing details on the workflows: DICOM->Full brain tractography / peritumoral (Demian)
# Refactoring of the tractography display widget (Isaiah)
# Laterality (Lauren)
# Selection for models and bundles post-clustering (Lauren)
#ROI-based / picking selection of fiber bundles (Maybe one of Sylvain's interns)
#Adding streamlined tractography to the Finsler front propagation tractography toolkit (Antonio)
#Add ODF estimation / visualization (Antonio)
# Workflows and Service Oriented Architecture Modules for Slicer4 as Extensions (Alexander Zaitsev, Wendy Plesniak, Ron Kikinis)
# [[2011_Summer_Project__Week_DICOM_Networking|DICOM Networking interface for Slicer4]] (Steve Pieper, Nicole Aucoin, Noby Hata)
# Stenosis Detector in 3D Slicer 4 (Suares Tamekue, Daniel Haehn, Luca Antiga)

==Background==

We are pleased to announce the 13th PROJECT WEEK of hands-on research and development activity for applications in Image-Guided Therapy, Neuroscience, and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants. If you would like to learn more about this event, please [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week click here to join our mailing list].

Active preparation begins on Thursday, April 28th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 40-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].

== Logistics ==
*'''Dates:''' June 20-24, 2011
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''REGISTRATION:''' Please register [http://guest.cvent.com/d/sdqy0l/4W here]. Payment must be made by credit card.
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week).
*'''Hotel:''' Boston Marriott Cambridge, Two Cambridge Center, 50 Broadway, Cambridge, MA 02142. Group rate is $199/night plus tax. Book [http://www.marriott.com/hotels/travel/boscb?groupCode=jrbjrba&app=resvlink&fromDate=6/19/11&toDate=6/24/11 here] or call 1-617-494-6600 and mention that you are booking in the MIT Room Block. '''All reservations must be made by May 29, 2011 to receive the discounted rate.'''

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 28, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on Thursday May 12, all participants to add a one line title of their project to #Projects
#By 3pm ET on Thursday June 9, all project leads to complete [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 16: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/#dirlist Slicer-3-6 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].