NAMIC Wiki - User contributions [en]

DTI Tractography Challenge MICCAI2011 Submission Format Sept18

2011-09-15T21:53:01Z

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*patient3:
patient3_left_tract_lastName.vtk 
patient3_right_tract_lastName.vtk 
patient3_left_enveloppe_lastName.nhdr 
patient3_left_enveloppe_lastName.raw 
patient3_right_enveloppe_lastName.nhdr 
patient3_right_enveloppe_lastName.raw 

patient3_left_tract_axial_view_lastName.png 
patient3_left_tract_coronal_view_lastName.png 
patient3_left_tract_sagittal_view_lastName.png 
patient3_right_tract_axial_view_lastName.png 
patient3_right_tract_coronal_view_lastName.png 
patient3_right_tract_sagittal_view_lastName.png 

patient3_left_and_right_tract_axial_view_lastName.png 
patient3_left_and_right_tract_coronal_view_lastName.png 
patient3_left_and_right_tract_sagittal_view_lastName.png 

patient3_neurosurgicalview_lastName..png 
... 
patient3_neurosurgicalview_lastName..png 

*patient4:
patient4_left_tract_lastName.vtk 
patient4_right_tract_lastName.vtk 
patient4_left_enveloppe_lastName.nhdr 
patient4_left_enveloppe_lastName.raw 
patient4_right_enveloppe_lastName.nhdr 
patient4_right_enveloppe_lastName.raw 

patient4_left_tract_axial_view_lastName.png 
patient4_left_tract_coronal_view_lastName.png 
patient4_left_tract_sagittal_view_lastName.png 
patient4_right_tract_axial_view_lastName.png 
patient4_right_tract_coronal_view_lastName.png 
patient4_right_tract_sagittal_view_lastName.png 

patient4_left_and_right_tract_axial_view_lastName.png 
patient4_left_and_right_tract_coronal_view_lastName.png 
patient4_left_and_right_tract_sagittal_view_lastName.png 

patient4_neurosurgicalview_lastName..png 
... 
patient4_neurosurgicalview_lastName..png

DTI Tractography Challenge Datasets

2011-06-09T20:42:28Z

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== Neurosurgical Datasets ==

'''Neurosurgical Case 1'''
*Clinical Case: Astrocytoma, World Health Organization (WHO) grade III
*Acquistion Parameters
Data were acquired on a 3.0-T scanner (EXCITE Signa scanner,
GE Medical System, Milwaukee, Wisconsin) with Excite 14.0 using an
8-channel head coil. 
T1 SPGR: TR=7500 ms; TE=30 ms; matrix 256x256; FOV 25.6 cm ; 1-mm slice thickness 
T2 GRE: TR=8000 ms; TE=98 ms; matrix 512x512; voxel size 0.5 x 0.5 x 1.5 mm 
DWI Singe shot EPI: TR=14 000ms; TE=30 ms; 31 gradient directions, 1 baseline ; b-value = 1000 s/mm2 ; matrix 128x128; 2.6 mm slice thickness 
Segmentation: The file patient1-tumor.nhdr & raw is labelmap which contains the segmented structures: label #1 represents the solid part of the tumor; label #2 represents the cystic part of the tumor.

'''Neurosurgical Case 2'''
*Clinical Case: Oligoastrocytoma,WHO grade II
*Acquistion Parameters
Data were acquired on a 3.0-T scanner (EXCITE Signa scanner,
GE Medical System, Milwaukee, Wisconsin) with Excite 14.0 using an
8-channel head coil. 
T1 SPGR: TR=7500 ms; TE=30 ms; matrix 256x256; FOV 25.6 cm ; 1-mm slice thickness 
T2 GRE: TR=8000 ms; TE=98 ms; matrix 512x512; voxel size 0.5 x 0.5 x 1.5 mm 
DWI Single shot EPI: TR=14 000ms; TE=30 ms; 55 gradient directions, 1 baseline ; b-value = 1000 s/mm2 ; matrix 128x128; 2.6 mm slice thickness 
Segmentation: The file patient2-tumor.nhdr & raw is labelmap which contains the segmented structures: label #1 represents the solid part of the tumor; label #2 represents the cystic part of the tumor.

'''Neurosurgical Case 3'''
*Clinical Case: Pending
*Acquisition Parameters:
*T1 Axial SPGR: matrix 256x256; voxel size 1 x 1 x 1.4 mm, volume size 256 x 256 x130
*T2 matrix 512x512; voxel size 0.5 x 0.5 x 1.5 mm, volume size 512 x 512 x 100
*DWI matrix 256 x256; voxel size 1 x 1 x 2.6 mm, 31 gradient directions, 1 baseline , b-value = 1000 s/mm2; volume size 256 x 256 x 32 x 52

'''Neurosurgical Case 4'''
*Clinical Case: Pending
*Acquisition Parameters:
*T1 Axial SPGR: matrix 256x256; voxel size 1 x 1 x 1.4 mm, volume size 256 x 256 x130
*T2 matrix 512x512; voxel size 0.5 x 0.5 x 1.5 mm, volume size 512 x 512 x 100
*DWI matrix 256 x256; voxel size 1 x 1 x 2.6 mm, 31 gradient directions, 1 baseline , b-value = 1000 s/mm2; volume size 256 x 256 x 32 x 52

== Control subjects Datasets==
Two adult control subject datasets will be available for this challenge. For each subject we have 10 repetitions of the structural and diffusion-weighted acquisitions. All scans were acquired on the same type of scanner (Siemens Tim Trio) at 5 different institutions.

Details of the DWI acquisition parameters:
* 25 gradient directions + 1 baseline
* Variable b-value (range between 40 and 1000): each diffusion weighted image has a different b value.
* Spacial resolution of 1.97x1.97x2mm
* Image size 96x96x81

Details of DTI estimation:
* Tensor estimation using weighted least square algorithm

Details of the structural acquisition. We provide two sets of images:
* Original T1 and T2 (size: 160x224x256, spacing: 1x1x1mm)
* T1 and T2 registered and resampled to baseline (size: 96x96x81, spacing: 1.97x1.97x2mm) (Affine + BSpline)

=='''File format and naming convention for submission'''==

The results should be sent in a zip archive or tarball file named ''''miccai2011DTIChallenge_firstAuthorName.zip''''.
For each case, the results should be submitted in the following formats: 1) 3D coordinate of the tracts: vtkPolydata ASCII VTK file format; 2) enveloppe of the tracts (voxelized binary image of the tracts): ITK-readable Nrrd file format 3) anatomical views (axial, coronal, sagittal) of individual and paired corticospinal tracts with a black background, in png file format, 4) a set of intuitive neurosurgical views in png file format.

'''All results (Nrrd and vtk files) should be in the original DWI image space'''.

An example of the naming convention to be used for Patient1 and HealthySubject1 is given below:

*Patient1:
patient1_left_tract.vtk 
patient1_right_tract.vtk 
patient1_left_enveloppe.nhdr 
patient1_left_enveloppe.raw 
patient1_right_enveloppe.nhdr 
patient1_right_enveloppe.raw 
... 
patient1_left_tract_axial_view.png 
patient1_left_tract_coronal_view.png 
patient1_left_tract_sagittal_view.png 
patient1_right_tract_axial_view.png 
patient1_right_tract_coronal_view.png 
patient1_right_tract_sagittal_view.png 
... 
patient1_left_and_right_tract_axial_view.png 
patient1_left_and_right_tract_coronal_view.png 
patient1_left_and_right_tract_sagittal_view.png 

patient1_neurosurgicalview1.png 
... 
patient1_neurosurgicalviewN.png 

*Healthy subject1
healthysubject1_scan01_left_tract.vtk 
healthysubject1_scan01_right_tract.vtk 
... 
healthysubject1_scan10_left_tract.vtk 
healthysubject1_scan10_right_tract.vtk 
healthysubject1_scan01_left_enveloppe.nhdr 
healthysubject1_scan01_left_enveloppe.raw 
... 
healthysubject1_scan10_left_enveloppe.nhdr 
healthysubject1_scan10_left_enveloppe.raw 
healthysubject1_scan01_right_enveloppe.nhdr 
healthysubject1_scan01_right_enveloppe.raw 
... 
healthysubject1_scan01_right_enveloppe.nhdr 
healthysubject1_scan01_right_enveloppe.raw 
... 
healthysubject1_scan01_left_tract_axial_view.png 
healthysubject1_scan01_right_tract_coronal_view.png 
patient1_left_tract_sagittal_view.png 
patient1_right_tract_axial_view.png 
patient1_right_tract_coronal_view.png 
patient1_right_tract_sagittal_view.png 
... 
patient1_left_and_right_tract_axial_view.png 
patient1_left_and_right_tract_coronal_view.png 
patient1_left_and_right_tract_sagittal_view.png 

Back to [[Events:_DTI_Tractography_Challenge_MICCAI_2011 | DTI Tractography Challenge MICCAI 2011]]

DTI Tractography Challenge Datasets

2011-05-12T23:01:48Z

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DTI Tractography Challenge Datasets

2011-05-11T22:52:37Z

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DTI Tractography Challenge Datasets

2011-05-11T16:39:02Z

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DTI Tractography Challenge Datasets

2011-05-11T16:32:14Z

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DTI Tractography Challenge Datasets

2011-05-11T16:19:25Z

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DTI Tractography Challenge Datasets

2011-05-11T16:19:13Z

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DTI Tractography Challenge Datasets

2011-04-06T23:27:24Z

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DTI Tractography Challenge Datasets

2011-04-06T22:00:11Z

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DTI Tractography Challenge Datasets

2011-03-31T22:04:45Z

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DTI Tractography Challenge Datasets

2011-03-31T21:41:01Z

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DTI Tractography Challenge Datasets

2011-03-28T21:38:53Z

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== Neurosurgical Datasets ==

*Neurosurgical Case 1
**Clinical Case Description
**Data Description
T1,T2,DWI,DTI : 
Segmentation: The file patient1-tumor.nhdr & raw is labelmap which contains the segmented structures: label #1 represents the solid part of the tumor; label #2 represents the cystic part of the tumor.

*Neurosurgical Case 2
**Clinical Case Description
**Data Description:

== Control subjects Datasets==
Two adult control subject datasets will be available for this challenge. For both subjects we have 10 repetitions of the DTI acquisitions. All scans were done on the same type of scanner at 5 different institutions.

Here are the details of the acquisition parameters:
* 25 directions + 1 B0
* Variable b-value (range between 50 and 1000) - Each diffusion weighted image has a different b value.
* Spacial resolution of 1.97x1.97x2mm
* Image size 96x96x81

=='''File format and naming convention for submission'''==
For each case, the results should be submitted in the following formats: 1) 3D coordinate of the tracts: vtkPolydata ASCII VTK file format; 2) enveloppe of the tracts: ITK-readable Nrrd file format
 Naming convention:
* zip archive file: miccaiDTIChallenge_firstAuthorName.zip
* VTK file: firstAuthorName_tract_coordinate.vtk
* Nrrd file: firstAuthorName_tract_enveloppe.nhdr and firstAuthorName_tract_enveloppe.nhdr
* PNG file: firstAuthorName_tract_axialView.png; firstAuthorName_tract_sagittalView.png; firstAuthorName_tract_coronalView.png

Back to [[Events:_DTI_Tractography_Challenge_MICCAI_2011 | DTI Tractography Challenge MICCAI 2011]]

NAMIC Tools Suite for DTI analysis

2010-06-24T20:29:49Z

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__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Iowa: Hans Johnson, Vincent Magnotta, Joy Matsui
* Utah: Sylvain Gouttard, Guido Gerig
* UNC: Clement Vachet, Yundi Shi, Francois Budin
* BWH: Demian Wassermann, Carl-Fredrik Westin
* GE: Xiaodong Tao

==Project==
<div style="margin: 10px;">
<div style="width: 30%; float: left; padding-right: 2%;">
<h3>Objective</h3>
The overall goal would be to improve the end user experience when using these tools by making them more consistent, more tolerant to various scanners and protocols, and improving the documentation for these tools.

We would like to have a single downloaded package that build consistently on Linux/Mac/Windows and provides at least a basic analysis that includes robust conversion from dicom to NRRD, quality control checking with DTI Prep, all the way through to regional scalar measures and generation of fiber tracts.
</div>

<div style="width: 30%; float: left; padding-right: 2%;">
<h3>Approach, Plan</h3>
Here are specifics troubles that we are currently having:

#Review http://wiki.na-mic.org/Wiki/index.php/AHM2010:DiffusionDatatypesBreakout
#DicomToNrrd often fails to convert data sets properly, and fixing one class of dicom data has often caused failures in other classes that had previously worked.
#A test suite needs to be created for DicomToNrrd to ensure that changes do not break backwards compatibilty
#Phillips data is often collected with non-identity measurement frames, some tools support that, some do not. Identify and correct the tools as necessary.
#Identify consisent set of fileformats to be used interoperably between tools
#Identify fibertracking tools.
#Idenfify tools that need to be create/migrated/incorporated modified.
#Write documentation to improve what is already on http://www.nitrc.org/plugins/mwiki/index.php/dtiprep:MainPage
#Create binary install packages for Linux/Mac/Windows
#Create a tutorial that walks though a complete analysis of data, including how to visually inspect failing test cases when gradient directions are improperly interpreted.

</div>

<div style="width: 35%; float: left;">
<h3>Progress</h3>

# Replaced several slightly different implementations of mutual information based registration (all of which were untested) with the highly tested and consistent implementation from BRAINSFit ( http://testing.psychiatry.uiowa.edu/CDash/index.php?project=BRAINSFit&date=2010-05-26 NOTE 67% code coverage!)
# Fixed the tools by : Serdar K Balci (serdar at csail.mit.edu): http://www.na-mic.org/svn/NAMICSandBox/trunk/MultiImageRegistration/ to properly respect image orientation so that it works properly with images with non-identity directions.
# Added Test Suite to MultiImageRegistration to ensure that correct results are preserved across platforms and code changes.
# Added MultiImageRegistration as option for to B0 averaging step in DTIPrep
# Divergent code in DTIPrep copied from GTRACT and DTIProcess was removed, and now depends directly on the libraries supplied by GTRACT and DTIProcess. This allows bug fixes in one to propogate to DTIPrep without extra effort.
# Added regression test suite to GTRACT
# The documentation for the whole DTIProcess has been written and updated in the corresponding xml files. Then this documentation has been converted into wiki format for the web site.
# We worked on the module to convert .fib fiber files to .vtk fiber files and vice versa. Integrate this module to the tools dealing with fibers.

Here is how I compiled the entire suite of tools as it currently stands

<pre>
svn co https://www.nitrc.org/svn/dtiprep/trunk AllDTIProcessing
mkdir AllDTIProcessing-build
cd AllDTIProcessing-build/
export QTDIR=/opt/qt-4.6.2/
ccmake ../AllDTIProcessing
make -j 16
</pre>

=====================================
This is done through CMAKE External packages, and build a consistent set of interoperable tools including:

ITK, VTK, DTIProcess, DicomToNrrdConverter, GTRACT, MuliImageRegistration, SlicerExecutionModel, and DTIPrep.

Note that DTIPrep depends upon libraries created from GTRACT and MultiImageRegistration, and binary executables created from DTIProcesss and DicomToNrrdConverter.

I’d like to add the QuantitativeFiberClustering tools into the mix also.

======================================
We will be arriving with over 200 scans from 15 different scanners, and 4 different scanning protocols, and we would like to make a process that simplifies processing and analysis of these data sets.

======================================

[http://www.nitrc.org/plugins/mwiki/index.php/vmagnotta:GTRACT_V4|GTRACT documentation]

</div>

Projects:DicomToNrrdForDTI

2008-04-29T17:29:06Z

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= Dicom conversion for DTI data =

== Introduction ==

In this page we present some results on the conversion from dicom data to DTI. Working with this new dataset, we noticed differences between the dicom header information and the ones from the original protocol designed for this study. In this page, we want describe and discuss these differences.

The data we worked with have been acquired with a Siemens 3T Tim Trio.

The DTI sequence is a 25 directions with variable b-values plus one B0 image.

[[Image:OrigDataBVal.png|thumb|400px|right]]
[[Image:OrigGradDir3D.png|thumb|400px|left|none|Original 25 gradient directions]]

== Data comparison ==

We loaded this dicom dataset into the “Dicom DWI loader” module in Slicer3. This module creates a NRRD header based on the information read from the dicom header. We compared the values outputted by the Slicer3 modules with the ones gave to us by the people who designed the DTI sequence.

=== bValues ===

The protocol specifies a bvalue maximum of bMax = 1000. Then the bvalue for each directions is bMax times the square of the gradient direction magnitude.

We found out that the bvalues that we read from the dicom header are rounded up to the nearest 50. However people from Siemens told us that the actual bvalues used for the acquisition are the correct ones. The bvalue is modified only when written in the dicom header. It seems that if a user does not have the protocol, it's not possible to find to proper, exact bvalues.

[[Image:BValComparison.png|thumb|400px|left]]
[[Image:BvalTable.png|thumb|300px|right|none|Bvalues comparison]]

=== Gradient directions ===

We noticed a major difference in the gradient direction encoding. When displaying the original vectors, they seem to be spread around the sphere. Whereas when we display the gradients of the dataset we worked with, they seem to be only on half of the plan. (in blue on the image)

[[Image:GradDirComp.png|thumb|400px|left|Dicom (blue) and Original (red) vectors displayed on the spehere]]
[[Image:GradDir_lineComp.png|thumb|400px|right|Dicom (blue) and Original (red) lines displayed on the spehere]]

We know that it's not the vector itself which is important for the tensor computation, but more the line held by the vector. When we display lines instead of vectors, we can see that most of the blue lines have a matching red line. There is no more than 3 degrees difference between the vectors.

But the actual values read from the dicom being different from the original sequence could be an issues for some kind of DTI processing.

=== Orientation ===

All the information for the image orientation are included in the dicom header. They are used to create the Nrrd header to process the dwi images.
When displaying the tensor we can see that the orientation is not correct. There is a flip along the X axis.

Here are the Nrrd header generated from dicom and its associated tensor visualization:`

<code><pre> NRRD0005
# Complete NRRD file format specification at:
# http://teem.sourceforge.net/nrrd/format.html
type: short
dimension: 4
space: right-anterior-superior
sizes: 26 96 96 81
space directions: none (-1.97917,0,0) (0,-1.97917,0) (0,0,-2)
kinds: list domain domain domain
endian: little
encoding: gzip
space origin: (48,48,40.5)
measurement frame: (1,0,0) (0,1,0) (0,0,1)
modality:=DWMRI
DWMRI_b-value:=1000.000000
DWMRI_gradient_0000:=0.000000 0.000000 0.000000
DWMRI_gradient_0001:=0.999310 -0.026261 -0.026261
DWMRI_gradient_0002:=-0.935465 0.003956 -0.353397
DWMRI_gradient_0003:=-0.935257 0.004295 0.353943
DWMRI_gradient_0004:=-0.808036 0.528933 0.259437
DWMRI_gradient_0005:=-0.576658 0.580108 -0.575274
DWMRI_gradient_0006:=-0.577350 -0.584657 -0.569950
DWMRI_gradient_0007:=-0.577350 -0.581504 0.573167
DWMRI_gradient_0008:=-0.497275 -0.852931 0.158826
DWMRI_gradient_0009:=-0.354696 0.934976 0.003268
DWMRI_gradient_0010:=-0.355116 0.934819 0.002524
DWMRI_gradient_0011:=0.309152 -0.857266 -0.411728
DWMRI_gradient_0012:=0.305705 -0.000966 0.952126
DWMRI_gradient_0013:=-0.307754 0.002441 0.951463
DWMRI_gradient_0014:=0.002371 0.527850 0.849334
DWMRI_gradient_0015:=0.001497 0.852692 -0.522412
DWMRI_gradient_0016:=0.005889 0.359783 -0.933016
DWMRI_gradient_0017:=0.002612 -0.359715 -0.933057
DWMRI_gradient_0018:=-0.307108 -0.853200 -0.421585
DWMRI_gradient_0019:=0.499156 0.528391 -0.686765
DWMRI_gradient_0020:=-0.499365 0.528606 -0.686448
DWMRI_gradient_0021:=0.496297 -0.854716 0.152151
DWMRI_gradient_0022:=0.577350 -0.581702 -0.572966
DWMRI_gradient_0023:=-0.807921 -0.529384 -0.258876
DWMRI_gradient_0024:=-0.809373 -0.002040 0.587291
DWMRI_gradient_0025:=-0.809376 -0.001631 -0.587289
</pre></code>

[[Image:TensorWrongOrientation.png|thumb|400px|none|Tensor display estimated straight from the dicom header information]]

If we switch the “measurement frame” from (1,0,0) (0,1,0) (0,0,1) to (-1,0,0) (0,1,0) (0,0,1) (flipping the X axis) the tensors “look right” and we can track fibers.

[[Image:TensorRightOrientation.png|thumb|400px|none|Tensor display estimated with corrected Nrrd header]]

== Conclusion ==

We just wanted to point out here the differences between the information embedded in the dicom header and the one inputted in the scanner when the sequence is designed.

File:TensorRightOrientation.png

2008-04-29T17:27:08Z

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File:TensorWrongOrientation.png

2008-04-29T17:24:53Z

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Projects:DicomToNrrdForDTI

2008-04-29T17:17:59Z

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File:GradDir lineComp.png

2008-04-29T17:16:35Z

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File:GradDirComp.png

2008-04-29T17:12:10Z

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Projects:DicomToNrrdForDTI

2008-04-29T17:10:57Z

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File:BvalTable.png

2008-04-29T17:09:36Z

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File:BValComparison.png

2008-04-29T17:07:31Z

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Projects:DicomToNrrdForDTI

2008-04-29T17:03:06Z

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Dicom conversion for DTI data

== Introduction ==

In this page we present some results on the conversion from dicom data to DTI. Working with this new dataset, we noticed differences between the dicom header information and the ones from the original protocol designed for this study. In this page, we want describe and discuss these differences.

The data we worked with have been acquired with a Siemens 3T Tim Trio.

The DTI sequence is a 25 directions with variable b-values plus one B0 image.

[[Image:OrigDataBVal.png|400px|right]]
[[Image:OrigGradDir3D.png|400px|left|none]]

== Data comparison ==

We loaded this dicom dataset into the “Dicom DWI loader” module in Slicer3. This module creates a NRRD header based on the information read from the dicom header. We compared the values outputted by the Slicer3 modules with the ones gave to us by the people who designed the DTI sequence.

= bValues =

Projects:DicomToNrrdForDTI

2008-04-29T16:57:04Z

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Projects:DicomToNrrdForDTI

2008-04-29T16:56:32Z

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Projects:DicomToNrrdForDTI

2008-04-29T16:55:41Z

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File:OrigGradDir3D.png

2008-04-29T16:52:11Z

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File:OrigDataBVal.png

2008-04-29T16:51:41Z

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Projects:DicomToNrrdForDTI

2008-04-29T16:50:32Z

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NA-MIC Internal Collaborations:DiffusionImageAnalysis

2008-04-25T21:53:35Z

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Back to [[NA-MIC_Internal_Collaborations|NA-MIC Internal Collaborations]]
__NOTOC__
= Diffusion Image Analysis =

=== Tractography Methods ===

{| cellpadding="10"
| style="width:15%" | [[Image:ZoomedResultWithModel.png|200px]]
| style="width:85%" |

== [[Projects:GeodesicTractographySegmentation|Geodesic Tractography Segmentation]] ==

In this work, we provide an energy minimization framework which allows one to find fiber tracts and volumetric fiber bundles in brain diffusion-weighted MRI (DW-MRI). [[Projects:GeodesicTractographySegmentation|More...]]

'''New: ''' J. Melonakos, E. Pichon, S. Angenet, and A. Tannenbaum. Finsler Active Contours. IEEE Transactions on Pattern Analysis and Machine Intelligence, 2007.

|-

| | [[Image:NAMIC callosum tracts prelim.jpg|200px]]
| |

== [[Projects:CorpusCallosumFiberTractography|Corpus Callosum Fiber Tractography]] ==

The goal of this project is to examine the integrity of fibers in the corpus callosum in patients with schizophrenia and determine whether this is associated with brain activation during memory tasks. [[Projects:CorpusCallosumFiberTractography|More...]]

'''New: ''' Wang P, Saykin A, Flashman L, Wishart H, Rabin L, Santulli R, McHugh T, MacDonald J, Mamourian A. [http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=1133 Regionally specific atrophy of the corpus callosum in AD, MCI and cognitive complaints.] Neurobiol Aging. 2006 Nov;27(11):1613-7.

|-

| | [[Image:MIT_DTI_JointSegReg_atlas3D.jpg|200px]]
| |

== [[Projects:DTIFiberRegistration|Joint Registration and Segmentation of DWI Fiber Tractography]] ==

The goal of this work is to jointly register and cluster DWI fiber tracts obtained from a group of subjects. [[Projects:DTIFiberRegistration|More...]]

'''New:''' Ziyan U, Sabuncu M, Grimson W, Westin C. [http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=1137 A Robust Algorithm for Fiber-Bundle Atlas Construction.] In Mathematical Methods in Biomedical Image Analysis (MMBIA 2007): 2007 IEEE Workshop, ICCV 2007 workshop. Rio de Janeiro, Brazil, 2007.

|-

| | [[Image:FiberTracts-angle.jpg|200px]]
| |

== [[Projects:DTIVolumetricWhiteMatterConnectivity|DTI Volumetric White Matter Connectivity]] ==

We have developed a PDE-based approach to white matter connectivity from DTI that is founded on the principal of minimal paths through the tensor volume. Our method computes a volumetric representation of a white matter tract given two endpoint regions. We have also developed statistical methods for quantifying the full tensor data along these pathways, which should be useful in clinical studies using DT-MRI. [[Projects:DTIVolumetricWhiteMatterConnectivity|More...]]

'''New: ''' Fletcher P, Tao R, Jeong W, Whitaker R. [http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=634 A volumetric approach to quantifying region-to-region white matter connectivity in diffusion tensor MRI.] Inf Process Med Imaging. 2007;20:346-358.

|-

| | [[Image:ConnectivityMap.png|200px]]
| |

== [[Projects:DTIStochasticTractography|Stochastic Tractography]] ==

This work calculates posterior distributions of white matter fiber tract parameters given diffusion observations in a DWI volume. [[Projects:DTIStochasticTractography|More...]]

|}

=== Clustering and Quantitative Analysis ===

{| cellpadding="10"
| style="width:15%" | [[Image:DTIQuantitativeAnalysis.png|200px]]
| style="width:85%" |

== [[Projects:DTIQuantitativeTractAnalysis|Quantitative Analysis of Fiber Tract Bundles]] ==

DT-MRI tractography can be used as a coordinate system for computing statistics of diffusion tensor data. The quantitative analysis of diffusion tensors takes into account the space of tensor measurements using a nonlinear Riemannian symmetric space framework. Tracts of interest are represented as a medial spline attributed with cross-sectional statistics. [[Projects:DTIQuantitativeTractAnalysis|More...]]

'''New: ''' Gilmore J, Lin W, Corouge I, Vetsa Y, Smith J, Kang C, Gu H, Hamer R, Lieberman J, Gerig G. [http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=905 Early Postnatal Development of Corpus Callosum and Corticospinal White Matter Assessed with Quantitative Tractography.] AJNR Am J Neuroradiol. 2007 Oct;28(9):1789-95.

|-

| | [[Image:CingulumAllSubjectsFibers.png|200px]]
| |

== [[Projects:DTIClustering|DTI Fiber Clustering and Fiber-Based Analysis]] ==

The goal of this project is to provide structural description of the white matter architecture as a partition into coherent fiber bundles and clusters, and to use these bundles for quantitative measurement. [[Projects:DTIClustering|More...]]

'''New:''' Monica E. Lemmond, Lauren J. O'Donnell, Stephen Whalen, Alexandra J. Golby. Characterizing Diffusion Along White Matter Tracts Affected by Primary Brain Tumors. Accepted to HBM 2007.

|-

| | [[Image:Models.jpg|200px]]
| |

== [[Projects:DTIModeling|Fiber Tract Modeling, Clustering, and Quantitative Analysis]] ==

The goal of this work is to model the shape of the fiber bundles and use this model discription in clustering and statistical analysis of fiber tracts. [[Projects:DTIModeling|More...]]

'''New:'''
M. Maddah, W. E. L. Grimson, S. K. Warfield, W. M. Wells, A Unified Framework for Clustering and Quantitative Analysis of White Matter Fiber Tracts. Medical Image Analysis, in press.

Maddah M, Wells W, Warfield S, Westin C, Grimson W. [http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=491 Probabilistic clustering and quantitative analysis of white matter fiber tracts.] Inf Process Med Imaging. 2007;20:372-83.

|-

| | [[Image:NAMIC UncinateFasiculus prelim.jpg|200px]]
| |

== [[Projects:FractionalAnisotrophyInTheUncinateFasciculus|Fractional Anisotropy in the Uncinate Fasciculus]] ==

Our objective is to measure the FA in the uncinate fasciculus in patients with schizophrenia. This project is based on the methods published by Kubicki et al. and extends that work by including a bipolar disorder control group, and determining whether there is an association between FA and cognitive functioning and symptoms in the patient groups. [[Projects:FractionalAnisotrophyInTheUncinateFasciculus|More...]]

'''New: ''' AHM 2007: Training on fiber tractography in Slicer with Sylvain Bouix that we can apply to this project as well as investigation of other fiber tracts such as the cingulate bundle.

|}

=== Other Diffusion Image Algorithms ===

{| cellpadding="10"
| style="width:15%" | [[Image:DartmouthPathOfInterest.png|200px]]
| style="width:85%" |

== [[Projects:IntegrityOfFrontoTemporalCircuitry|Integrity of Fronto-Temporal Circuitry]] ==

Our objective is to develop methodology that will permit investigators to specify functional MRI regional of interests (fROI) and determine the optimal white matter pathways between the fROIs based on DTI. [[Projects:IntegrityOfFrontoTemporalCircuitry|More...]]

'''New: ''' AHM 2007: John West had training session with Dennis Jen on new version of POI algorithm. Worked together to read new Dartmouth 3T Philips Data. Further work ongoing to integrate POI into Slicer 3.

|-

| | [[Image:Thalamus_algo_outline.png|200px]]
| |

== [[Projects:DTISegmentation|DTI-based Segmentation]] ==

Unlike conventional MRI, DTI provides adequate contrast to segment the thalamic nuclei, which are gray matter structures. [[Projects:DTISegmentation|More...]]

'''New:''' Ziyan U, Tuch D, Westin C. [http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=47 Segmentation of Thalamic Nuclei from DTI Using Spectral Clustering.] Proceedings of the 9th International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2006, LNCS 4191, pp. 807-814, 2006.Segmentation of Thalamic Nuclei from DTI using Spectral Clustering. Accepted to MICCAI 2006.

|-

| | [[Image:DTINoiseStatistics.png|200px]]
| |

== [[Projects:DTINoiseStatistics|Influence of Imaging Noise on DTI Statistics]] ==

Clinical acquisition of diffusion weighted images with high signal to noise ratio remains a challenge. The goal of this project is to understand the impact of MR noise on quantiative statistics of diffusion properties such as anisotropy measures, trace, etc. [[Projects:DTINoiseStatistics|More...]]

'''New: ''' Goodlett C, Fletcher P, Lin W, Gerig G. [http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=1074 Quantification of Measurement Error in DTI: Theoretical Predictions and Validation.] Proceedings of the 10th International Conference on Medical Image Computing and Computer Assisted Intervention, MICCAI 2007, LNCS 4791, pp. 10–17, 2007.

|-

| |
| |

== [[Projects:DicomToNrrdForDTI|Notes on the dicom conversion for DTI data]] ==

Report about some observation when converting DTI data from dicom to dwi volumes
[[Projects:DicomToNrrdForDTI|More...]]

|}

=== Validation ===

[[Image:Cingulum1.jpg|200px]]

== [[ProjectWeek200706:ContrastingTractographyMeasures|Contrasting Tractography Measures]] ==

This project represents a new initiative to build upon a shared vision among Cores 1, 3 and 5 that the field of medical image analysis would be well served by work in the area of validation, calibration and assessment of reliability in DW-MRI image analysis. [[ProjectWeek200706:ContrastingTractographyMeasures|More...]]

'''New: ''' [[SanteFe.Tractography.Conference|Contrasting Tractography Methods Conference]], Santa Fe, October 1-2, 2007.

{| cellpadding="10"
| style="width:15%" | [[Image:MBIRNseedROIcc1.png|200px]]
| style="width:85%" |

== [[Projects:DTIValidation|DTI Validation]] ==

To carry out quantitative and qualitative validation of the DTI tractography tools. These will be applied to a limited set of specific tracts in single data sets and single tractography tools, and on several data sets using at least two tractography programs and by investigators in different laboratories. [[Projects:DTIValidation|More...]]

 Future research is needed to establish critical values for diffusion sequence acquisition parameters that would allow diffusion data processing via Slicer.

|}

NA-MIC Internal Collaborations:DiffusionImageAnalysis

2008-04-25T21:52:55Z

Sgouttard:

Back to [[NA-MIC_Internal_Collaborations|NA-MIC Internal Collaborations]]
__NOTOC__
= Diffusion Image Analysis =

=== Tractography Methods ===

{| cellpadding="10"
| style="width:15%" | [[Image:ZoomedResultWithModel.png|200px]]
| style="width:85%" |

== [[Projects:GeodesicTractographySegmentation|Geodesic Tractography Segmentation]] ==

In this work, we provide an energy minimization framework which allows one to find fiber tracts and volumetric fiber bundles in brain diffusion-weighted MRI (DW-MRI). [[Projects:GeodesicTractographySegmentation|More...]]

'''New: ''' J. Melonakos, E. Pichon, S. Angenet, and A. Tannenbaum. Finsler Active Contours. IEEE Transactions on Pattern Analysis and Machine Intelligence, 2007.

|-

| | [[Image:NAMIC callosum tracts prelim.jpg|200px]]
| |

== [[Projects:CorpusCallosumFiberTractography|Corpus Callosum Fiber Tractography]] ==

The goal of this project is to examine the integrity of fibers in the corpus callosum in patients with schizophrenia and determine whether this is associated with brain activation during memory tasks. [[Projects:CorpusCallosumFiberTractography|More...]]

'''New: ''' Wang P, Saykin A, Flashman L, Wishart H, Rabin L, Santulli R, McHugh T, MacDonald J, Mamourian A. [http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=1133 Regionally specific atrophy of the corpus callosum in AD, MCI and cognitive complaints.] Neurobiol Aging. 2006 Nov;27(11):1613-7.

|-

| | [[Image:MIT_DTI_JointSegReg_atlas3D.jpg|200px]]
| |

== [[Projects:DTIFiberRegistration|Joint Registration and Segmentation of DWI Fiber Tractography]] ==

The goal of this work is to jointly register and cluster DWI fiber tracts obtained from a group of subjects. [[Projects:DTIFiberRegistration|More...]]

'''New:''' Ziyan U, Sabuncu M, Grimson W, Westin C. [http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=1137 A Robust Algorithm for Fiber-Bundle Atlas Construction.] In Mathematical Methods in Biomedical Image Analysis (MMBIA 2007): 2007 IEEE Workshop, ICCV 2007 workshop. Rio de Janeiro, Brazil, 2007.

|-

| | [[Image:FiberTracts-angle.jpg|200px]]
| |

== [[Projects:DTIVolumetricWhiteMatterConnectivity|DTI Volumetric White Matter Connectivity]] ==

We have developed a PDE-based approach to white matter connectivity from DTI that is founded on the principal of minimal paths through the tensor volume. Our method computes a volumetric representation of a white matter tract given two endpoint regions. We have also developed statistical methods for quantifying the full tensor data along these pathways, which should be useful in clinical studies using DT-MRI. [[Projects:DTIVolumetricWhiteMatterConnectivity|More...]]

'''New: ''' Fletcher P, Tao R, Jeong W, Whitaker R. [http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=634 A volumetric approach to quantifying region-to-region white matter connectivity in diffusion tensor MRI.] Inf Process Med Imaging. 2007;20:346-358.

|-

| | [[Image:ConnectivityMap.png|200px]]
| |

== [[Projects:DTIStochasticTractography|Stochastic Tractography]] ==

This work calculates posterior distributions of white matter fiber tract parameters given diffusion observations in a DWI volume. [[Projects:DTIStochasticTractography|More...]]

|}

=== Clustering and Quantitative Analysis ===

{| cellpadding="10"
| style="width:15%" | [[Image:DTIQuantitativeAnalysis.png|200px]]
| style="width:85%" |

== [[Projects:DTIQuantitativeTractAnalysis|Quantitative Analysis of Fiber Tract Bundles]] ==

DT-MRI tractography can be used as a coordinate system for computing statistics of diffusion tensor data. The quantitative analysis of diffusion tensors takes into account the space of tensor measurements using a nonlinear Riemannian symmetric space framework. Tracts of interest are represented as a medial spline attributed with cross-sectional statistics. [[Projects:DTIQuantitativeTractAnalysis|More...]]

'''New: ''' Gilmore J, Lin W, Corouge I, Vetsa Y, Smith J, Kang C, Gu H, Hamer R, Lieberman J, Gerig G. [http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=905 Early Postnatal Development of Corpus Callosum and Corticospinal White Matter Assessed with Quantitative Tractography.] AJNR Am J Neuroradiol. 2007 Oct;28(9):1789-95.

|-

| | [[Image:CingulumAllSubjectsFibers.png|200px]]
| |

== [[Projects:DTIClustering|DTI Fiber Clustering and Fiber-Based Analysis]] ==

The goal of this project is to provide structural description of the white matter architecture as a partition into coherent fiber bundles and clusters, and to use these bundles for quantitative measurement. [[Projects:DTIClustering|More...]]

'''New:''' Monica E. Lemmond, Lauren J. O'Donnell, Stephen Whalen, Alexandra J. Golby. Characterizing Diffusion Along White Matter Tracts Affected by Primary Brain Tumors. Accepted to HBM 2007.

|-

| | [[Image:Models.jpg|200px]]
| |

== [[Projects:DTIModeling|Fiber Tract Modeling, Clustering, and Quantitative Analysis]] ==

The goal of this work is to model the shape of the fiber bundles and use this model discription in clustering and statistical analysis of fiber tracts. [[Projects:DTIModeling|More...]]

'''New:'''
M. Maddah, W. E. L. Grimson, S. K. Warfield, W. M. Wells, A Unified Framework for Clustering and Quantitative Analysis of White Matter Fiber Tracts. Medical Image Analysis, in press.

Maddah M, Wells W, Warfield S, Westin C, Grimson W. [http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=491 Probabilistic clustering and quantitative analysis of white matter fiber tracts.] Inf Process Med Imaging. 2007;20:372-83.

|-

| | [[Image:NAMIC UncinateFasiculus prelim.jpg|200px]]
| |

== [[Projects:FractionalAnisotrophyInTheUncinateFasciculus|Fractional Anisotropy in the Uncinate Fasciculus]] ==

Our objective is to measure the FA in the uncinate fasciculus in patients with schizophrenia. This project is based on the methods published by Kubicki et al. and extends that work by including a bipolar disorder control group, and determining whether there is an association between FA and cognitive functioning and symptoms in the patient groups. [[Projects:FractionalAnisotrophyInTheUncinateFasciculus|More...]]

'''New: ''' AHM 2007: Training on fiber tractography in Slicer with Sylvain Bouix that we can apply to this project as well as investigation of other fiber tracts such as the cingulate bundle.

|}

=== Other Diffusion Image Algorithms ===

{| cellpadding="10"
| style="width:15%" | [[Image:DartmouthPathOfInterest.png|200px]]
| style="width:85%" |

== [[Projects:IntegrityOfFrontoTemporalCircuitry|Integrity of Fronto-Temporal Circuitry]] ==

Our objective is to develop methodology that will permit investigators to specify functional MRI regional of interests (fROI) and determine the optimal white matter pathways between the fROIs based on DTI. [[Projects:IntegrityOfFrontoTemporalCircuitry|More...]]

'''New: ''' AHM 2007: John West had training session with Dennis Jen on new version of POI algorithm. Worked together to read new Dartmouth 3T Philips Data. Further work ongoing to integrate POI into Slicer 3.

|-

| | [[Image:Thalamus_algo_outline.png|200px]]
| |

== [[Projects:DTISegmentation|DTI-based Segmentation]] ==

Unlike conventional MRI, DTI provides adequate contrast to segment the thalamic nuclei, which are gray matter structures. [[Projects:DTISegmentation|More...]]

'''New:''' Ziyan U, Tuch D, Westin C. [http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=47 Segmentation of Thalamic Nuclei from DTI Using Spectral Clustering.] Proceedings of the 9th International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2006, LNCS 4191, pp. 807-814, 2006.Segmentation of Thalamic Nuclei from DTI using Spectral Clustering. Accepted to MICCAI 2006.

|-

| | [[Image:DTINoiseStatistics.png|200px]]
| |

== [[Projects:DTINoiseStatistics|Influence of Imaging Noise on DTI Statistics]] ==

Clinical acquisition of diffusion weighted images with high signal to noise ratio remains a challenge. The goal of this project is to understand the impact of MR noise on quantiative statistics of diffusion properties such as anisotropy measures, trace, etc. [[Projects:DTINoiseStatistics|More...]]

'''New: ''' Goodlett C, Fletcher P, Lin W, Gerig G. [http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=1074 Quantification of Measurement Error in DTI: Theoretical Predictions and Validation.] Proceedings of the 10th International Conference on Medical Image Computing and Computer Assisted Intervention, MICCAI 2007, LNCS 4791, pp. 10–17, 2007.

|-

| |

== [[Projects:DicomToNrrdForDTI|Notes on the dicom conversion for DTI data]] ==

Report about some observation when converting DTI data from dicom to dwi volumes
[[Projects:DicomToNrrdForDTI|More...]]

|}

=== Validation ===

[[Image:Cingulum1.jpg|200px]]

== [[ProjectWeek200706:ContrastingTractographyMeasures|Contrasting Tractography Measures]] ==

This project represents a new initiative to build upon a shared vision among Cores 1, 3 and 5 that the field of medical image analysis would be well served by work in the area of validation, calibration and assessment of reliability in DW-MRI image analysis. [[ProjectWeek200706:ContrastingTractographyMeasures|More...]]

'''New: ''' [[SanteFe.Tractography.Conference|Contrasting Tractography Methods Conference]], Santa Fe, October 1-2, 2007.

{| cellpadding="10"
| style="width:15%" | [[Image:MBIRNseedROIcc1.png|200px]]
| style="width:85%" |

== [[Projects:DTIValidation|DTI Validation]] ==

To carry out quantitative and qualitative validation of the DTI tractography tools. These will be applied to a limited set of specific tracts in single data sets and single tractography tools, and on several data sets using at least two tractography programs and by investigators in different laboratories. [[Projects:DTIValidation|More...]]

 Future research is needed to establish critical values for diffusion sequence acquisition parameters that would allow diffusion data processing via Slicer.

|}

NA-MIC Internal Collaborations:DiffusionImageAnalysis

2008-04-25T21:51:51Z

Sgouttard:

Back to [[NA-MIC_Internal_Collaborations|NA-MIC Internal Collaborations]]
__NOTOC__
= Diffusion Image Analysis =

=== Tractography Methods ===

{| cellpadding="10"
| style="width:15%" | [[Image:ZoomedResultWithModel.png|200px]]
| style="width:85%" |

== [[Projects:GeodesicTractographySegmentation|Geodesic Tractography Segmentation]] ==

In this work, we provide an energy minimization framework which allows one to find fiber tracts and volumetric fiber bundles in brain diffusion-weighted MRI (DW-MRI). [[Projects:GeodesicTractographySegmentation|More...]]

'''New: ''' J. Melonakos, E. Pichon, S. Angenet, and A. Tannenbaum. Finsler Active Contours. IEEE Transactions on Pattern Analysis and Machine Intelligence, 2007.

|-

| | [[Image:NAMIC callosum tracts prelim.jpg|200px]]
| |

== [[Projects:CorpusCallosumFiberTractography|Corpus Callosum Fiber Tractography]] ==

The goal of this project is to examine the integrity of fibers in the corpus callosum in patients with schizophrenia and determine whether this is associated with brain activation during memory tasks. [[Projects:CorpusCallosumFiberTractography|More...]]

'''New: ''' Wang P, Saykin A, Flashman L, Wishart H, Rabin L, Santulli R, McHugh T, MacDonald J, Mamourian A. [http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=1133 Regionally specific atrophy of the corpus callosum in AD, MCI and cognitive complaints.] Neurobiol Aging. 2006 Nov;27(11):1613-7.

|-

| | [[Image:MIT_DTI_JointSegReg_atlas3D.jpg|200px]]
| |

== [[Projects:DTIFiberRegistration|Joint Registration and Segmentation of DWI Fiber Tractography]] ==

The goal of this work is to jointly register and cluster DWI fiber tracts obtained from a group of subjects. [[Projects:DTIFiberRegistration|More...]]

'''New:''' Ziyan U, Sabuncu M, Grimson W, Westin C. [http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=1137 A Robust Algorithm for Fiber-Bundle Atlas Construction.] In Mathematical Methods in Biomedical Image Analysis (MMBIA 2007): 2007 IEEE Workshop, ICCV 2007 workshop. Rio de Janeiro, Brazil, 2007.

|-

| | [[Image:FiberTracts-angle.jpg|200px]]
| |

== [[Projects:DTIVolumetricWhiteMatterConnectivity|DTI Volumetric White Matter Connectivity]] ==

We have developed a PDE-based approach to white matter connectivity from DTI that is founded on the principal of minimal paths through the tensor volume. Our method computes a volumetric representation of a white matter tract given two endpoint regions. We have also developed statistical methods for quantifying the full tensor data along these pathways, which should be useful in clinical studies using DT-MRI. [[Projects:DTIVolumetricWhiteMatterConnectivity|More...]]

'''New: ''' Fletcher P, Tao R, Jeong W, Whitaker R. [http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=634 A volumetric approach to quantifying region-to-region white matter connectivity in diffusion tensor MRI.] Inf Process Med Imaging. 2007;20:346-358.

|-

| | [[Image:ConnectivityMap.png|200px]]
| |

== [[Projects:DTIStochasticTractography|Stochastic Tractography]] ==

This work calculates posterior distributions of white matter fiber tract parameters given diffusion observations in a DWI volume. [[Projects:DTIStochasticTractography|More...]]

|}

=== Clustering and Quantitative Analysis ===

{| cellpadding="10"
| style="width:15%" | [[Image:DTIQuantitativeAnalysis.png|200px]]
| style="width:85%" |

== [[Projects:DTIQuantitativeTractAnalysis|Quantitative Analysis of Fiber Tract Bundles]] ==

DT-MRI tractography can be used as a coordinate system for computing statistics of diffusion tensor data. The quantitative analysis of diffusion tensors takes into account the space of tensor measurements using a nonlinear Riemannian symmetric space framework. Tracts of interest are represented as a medial spline attributed with cross-sectional statistics. [[Projects:DTIQuantitativeTractAnalysis|More...]]

'''New: ''' Gilmore J, Lin W, Corouge I, Vetsa Y, Smith J, Kang C, Gu H, Hamer R, Lieberman J, Gerig G. [http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=905 Early Postnatal Development of Corpus Callosum and Corticospinal White Matter Assessed with Quantitative Tractography.] AJNR Am J Neuroradiol. 2007 Oct;28(9):1789-95.

|-

| | [[Image:CingulumAllSubjectsFibers.png|200px]]
| |

== [[Projects:DTIClustering|DTI Fiber Clustering and Fiber-Based Analysis]] ==

The goal of this project is to provide structural description of the white matter architecture as a partition into coherent fiber bundles and clusters, and to use these bundles for quantitative measurement. [[Projects:DTIClustering|More...]]

'''New:''' Monica E. Lemmond, Lauren J. O'Donnell, Stephen Whalen, Alexandra J. Golby. Characterizing Diffusion Along White Matter Tracts Affected by Primary Brain Tumors. Accepted to HBM 2007.

|-

| | [[Image:Models.jpg|200px]]
| |

== [[Projects:DTIModeling|Fiber Tract Modeling, Clustering, and Quantitative Analysis]] ==

The goal of this work is to model the shape of the fiber bundles and use this model discription in clustering and statistical analysis of fiber tracts. [[Projects:DTIModeling|More...]]

'''New:'''
M. Maddah, W. E. L. Grimson, S. K. Warfield, W. M. Wells, A Unified Framework for Clustering and Quantitative Analysis of White Matter Fiber Tracts. Medical Image Analysis, in press.

Maddah M, Wells W, Warfield S, Westin C, Grimson W. [http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=491 Probabilistic clustering and quantitative analysis of white matter fiber tracts.] Inf Process Med Imaging. 2007;20:372-83.

|-

| | [[Image:NAMIC UncinateFasiculus prelim.jpg|200px]]
| |

== [[Projects:FractionalAnisotrophyInTheUncinateFasciculus|Fractional Anisotropy in the Uncinate Fasciculus]] ==

Our objective is to measure the FA in the uncinate fasciculus in patients with schizophrenia. This project is based on the methods published by Kubicki et al. and extends that work by including a bipolar disorder control group, and determining whether there is an association between FA and cognitive functioning and symptoms in the patient groups. [[Projects:FractionalAnisotrophyInTheUncinateFasciculus|More...]]

'''New: ''' AHM 2007: Training on fiber tractography in Slicer with Sylvain Bouix that we can apply to this project as well as investigation of other fiber tracts such as the cingulate bundle.

|}

=== Other Diffusion Image Algorithms ===

{| cellpadding="10"
| style="width:15%" | [[Image:DartmouthPathOfInterest.png|200px]]
| style="width:85%" |

== [[Projects:IntegrityOfFrontoTemporalCircuitry|Integrity of Fronto-Temporal Circuitry]] ==

Our objective is to develop methodology that will permit investigators to specify functional MRI regional of interests (fROI) and determine the optimal white matter pathways between the fROIs based on DTI. [[Projects:IntegrityOfFrontoTemporalCircuitry|More...]]

'''New: ''' AHM 2007: John West had training session with Dennis Jen on new version of POI algorithm. Worked together to read new Dartmouth 3T Philips Data. Further work ongoing to integrate POI into Slicer 3.

|-

| | [[Image:Thalamus_algo_outline.png|200px]]
| |

== [[Projects:DTISegmentation|DTI-based Segmentation]] ==

Unlike conventional MRI, DTI provides adequate contrast to segment the thalamic nuclei, which are gray matter structures. [[Projects:DTISegmentation|More...]]

'''New:''' Ziyan U, Tuch D, Westin C. [http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=47 Segmentation of Thalamic Nuclei from DTI Using Spectral Clustering.] Proceedings of the 9th International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2006, LNCS 4191, pp. 807-814, 2006.Segmentation of Thalamic Nuclei from DTI using Spectral Clustering. Accepted to MICCAI 2006.

|-

| | [[Image:DTINoiseStatistics.png|200px]]
| |

== [[Projects:DTINoiseStatistics|Influence of Imaging Noise on DTI Statistics]] ==

Clinical acquisition of diffusion weighted images with high signal to noise ratio remains a challenge. The goal of this project is to understand the impact of MR noise on quantiative statistics of diffusion properties such as anisotropy measures, trace, etc. [[Projects:DTINoiseStatistics|More...]]

'''New: ''' Goodlett C, Fletcher P, Lin W, Gerig G. [http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=1074 Quantification of Measurement Error in DTI: Theoretical Predictions and Validation.] Proceedings of the 10th International Conference on Medical Image Computing and Computer Assisted Intervention, MICCAI 2007, LNCS 4791, pp. 10–17, 2007.

|-

== [[Projects:DicomToNrrdForDTI|Notes on the dicom conversion for DTI data]] ==

Report about some observation when converting DTI data from dicom to dwi volumes
[[Projects:DicomToNrrdForDTI|More...]]

|}

=== Validation ===

[[Image:Cingulum1.jpg|200px]]

== [[ProjectWeek200706:ContrastingTractographyMeasures|Contrasting Tractography Measures]] ==

This project represents a new initiative to build upon a shared vision among Cores 1, 3 and 5 that the field of medical image analysis would be well served by work in the area of validation, calibration and assessment of reliability in DW-MRI image analysis. [[ProjectWeek200706:ContrastingTractographyMeasures|More...]]

'''New: ''' [[SanteFe.Tractography.Conference|Contrasting Tractography Methods Conference]], Santa Fe, October 1-2, 2007.

{| cellpadding="10"
| style="width:15%" | [[Image:MBIRNseedROIcc1.png|200px]]
| style="width:85%" |

== [[Projects:DTIValidation|DTI Validation]] ==

To carry out quantitative and qualitative validation of the DTI tractography tools. These will be applied to a limited set of specific tracts in single data sets and single tractography tools, and on several data sets using at least two tractography programs and by investigators in different laboratories. [[Projects:DTIValidation|More...]]

 Future research is needed to establish critical values for diffusion sequence acquisition parameters that would allow diffusion data processing via Slicer.

|}

NA-MIC Internal Collaborations:DiffusionImageAnalysis

2008-04-25T21:51:06Z

Sgouttard:

Back to [[NA-MIC_Internal_Collaborations|NA-MIC Internal Collaborations]]
__NOTOC__
= Diffusion Image Analysis =

=== Tractography Methods ===

{| cellpadding="10"
| style="width:15%" | [[Image:ZoomedResultWithModel.png|200px]]
| style="width:85%" |

== [[Projects:GeodesicTractographySegmentation|Geodesic Tractography Segmentation]] ==

In this work, we provide an energy minimization framework which allows one to find fiber tracts and volumetric fiber bundles in brain diffusion-weighted MRI (DW-MRI). [[Projects:GeodesicTractographySegmentation|More...]]

'''New: ''' J. Melonakos, E. Pichon, S. Angenet, and A. Tannenbaum. Finsler Active Contours. IEEE Transactions on Pattern Analysis and Machine Intelligence, 2007.

|-

| | [[Image:NAMIC callosum tracts prelim.jpg|200px]]
| |

== [[Projects:CorpusCallosumFiberTractography|Corpus Callosum Fiber Tractography]] ==

The goal of this project is to examine the integrity of fibers in the corpus callosum in patients with schizophrenia and determine whether this is associated with brain activation during memory tasks. [[Projects:CorpusCallosumFiberTractography|More...]]

'''New: ''' Wang P, Saykin A, Flashman L, Wishart H, Rabin L, Santulli R, McHugh T, MacDonald J, Mamourian A. [http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=1133 Regionally specific atrophy of the corpus callosum in AD, MCI and cognitive complaints.] Neurobiol Aging. 2006 Nov;27(11):1613-7.

|-

| | [[Image:MIT_DTI_JointSegReg_atlas3D.jpg|200px]]
| |

== [[Projects:DTIFiberRegistration|Joint Registration and Segmentation of DWI Fiber Tractography]] ==

The goal of this work is to jointly register and cluster DWI fiber tracts obtained from a group of subjects. [[Projects:DTIFiberRegistration|More...]]

'''New:''' Ziyan U, Sabuncu M, Grimson W, Westin C. [http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=1137 A Robust Algorithm for Fiber-Bundle Atlas Construction.] In Mathematical Methods in Biomedical Image Analysis (MMBIA 2007): 2007 IEEE Workshop, ICCV 2007 workshop. Rio de Janeiro, Brazil, 2007.

|-

| | [[Image:FiberTracts-angle.jpg|200px]]
| |

== [[Projects:DTIVolumetricWhiteMatterConnectivity|DTI Volumetric White Matter Connectivity]] ==

We have developed a PDE-based approach to white matter connectivity from DTI that is founded on the principal of minimal paths through the tensor volume. Our method computes a volumetric representation of a white matter tract given two endpoint regions. We have also developed statistical methods for quantifying the full tensor data along these pathways, which should be useful in clinical studies using DT-MRI. [[Projects:DTIVolumetricWhiteMatterConnectivity|More...]]

'''New: ''' Fletcher P, Tao R, Jeong W, Whitaker R. [http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=634 A volumetric approach to quantifying region-to-region white matter connectivity in diffusion tensor MRI.] Inf Process Med Imaging. 2007;20:346-358.

|-

| | [[Image:ConnectivityMap.png|200px]]
| |

== [[Projects:DTIStochasticTractography|Stochastic Tractography]] ==

This work calculates posterior distributions of white matter fiber tract parameters given diffusion observations in a DWI volume. [[Projects:DTIStochasticTractography|More...]]

|}

=== Clustering and Quantitative Analysis ===

{| cellpadding="10"
| style="width:15%" | [[Image:DTIQuantitativeAnalysis.png|200px]]
| style="width:85%" |

== [[Projects:DTIQuantitativeTractAnalysis|Quantitative Analysis of Fiber Tract Bundles]] ==

DT-MRI tractography can be used as a coordinate system for computing statistics of diffusion tensor data. The quantitative analysis of diffusion tensors takes into account the space of tensor measurements using a nonlinear Riemannian symmetric space framework. Tracts of interest are represented as a medial spline attributed with cross-sectional statistics. [[Projects:DTIQuantitativeTractAnalysis|More...]]

'''New: ''' Gilmore J, Lin W, Corouge I, Vetsa Y, Smith J, Kang C, Gu H, Hamer R, Lieberman J, Gerig G. [http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=905 Early Postnatal Development of Corpus Callosum and Corticospinal White Matter Assessed with Quantitative Tractography.] AJNR Am J Neuroradiol. 2007 Oct;28(9):1789-95.

|-

| | [[Image:CingulumAllSubjectsFibers.png|200px]]
| |

== [[Projects:DTIClustering|DTI Fiber Clustering and Fiber-Based Analysis]] ==

The goal of this project is to provide structural description of the white matter architecture as a partition into coherent fiber bundles and clusters, and to use these bundles for quantitative measurement. [[Projects:DTIClustering|More...]]

'''New:''' Monica E. Lemmond, Lauren J. O'Donnell, Stephen Whalen, Alexandra J. Golby. Characterizing Diffusion Along White Matter Tracts Affected by Primary Brain Tumors. Accepted to HBM 2007.

|-

| | [[Image:Models.jpg|200px]]
| |

== [[Projects:DTIModeling|Fiber Tract Modeling, Clustering, and Quantitative Analysis]] ==

The goal of this work is to model the shape of the fiber bundles and use this model discription in clustering and statistical analysis of fiber tracts. [[Projects:DTIModeling|More...]]

'''New:'''
M. Maddah, W. E. L. Grimson, S. K. Warfield, W. M. Wells, A Unified Framework for Clustering and Quantitative Analysis of White Matter Fiber Tracts. Medical Image Analysis, in press.

Maddah M, Wells W, Warfield S, Westin C, Grimson W. [http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=491 Probabilistic clustering and quantitative analysis of white matter fiber tracts.] Inf Process Med Imaging. 2007;20:372-83.

|-

| | [[Image:NAMIC UncinateFasiculus prelim.jpg|200px]]
| |

== [[Projects:FractionalAnisotrophyInTheUncinateFasciculus|Fractional Anisotropy in the Uncinate Fasciculus]] ==

Our objective is to measure the FA in the uncinate fasciculus in patients with schizophrenia. This project is based on the methods published by Kubicki et al. and extends that work by including a bipolar disorder control group, and determining whether there is an association between FA and cognitive functioning and symptoms in the patient groups. [[Projects:FractionalAnisotrophyInTheUncinateFasciculus|More...]]

'''New: ''' AHM 2007: Training on fiber tractography in Slicer with Sylvain Bouix that we can apply to this project as well as investigation of other fiber tracts such as the cingulate bundle.

|}

=== Other Diffusion Image Algorithms ===

{| cellpadding="10"
| style="width:15%" | [[Image:DartmouthPathOfInterest.png|200px]]
| style="width:85%" |

== [[Projects:IntegrityOfFrontoTemporalCircuitry|Integrity of Fronto-Temporal Circuitry]] ==

Our objective is to develop methodology that will permit investigators to specify functional MRI regional of interests (fROI) and determine the optimal white matter pathways between the fROIs based on DTI. [[Projects:IntegrityOfFrontoTemporalCircuitry|More...]]

'''New: ''' AHM 2007: John West had training session with Dennis Jen on new version of POI algorithm. Worked together to read new Dartmouth 3T Philips Data. Further work ongoing to integrate POI into Slicer 3.

|-

| | [[Image:Thalamus_algo_outline.png|200px]]
| |

== [[Projects:DTISegmentation|DTI-based Segmentation]] ==

Unlike conventional MRI, DTI provides adequate contrast to segment the thalamic nuclei, which are gray matter structures. [[Projects:DTISegmentation|More...]]

'''New:''' Ziyan U, Tuch D, Westin C. [http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=47 Segmentation of Thalamic Nuclei from DTI Using Spectral Clustering.] Proceedings of the 9th International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2006, LNCS 4191, pp. 807-814, 2006.Segmentation of Thalamic Nuclei from DTI using Spectral Clustering. Accepted to MICCAI 2006.

|-

| | [[Image:DTINoiseStatistics.png|200px]]
| |

== [[Projects:DTINoiseStatistics|Influence of Imaging Noise on DTI Statistics]] ==

Clinical acquisition of diffusion weighted images with high signal to noise ratio remains a challenge. The goal of this project is to understand the impact of MR noise on quantiative statistics of diffusion properties such as anisotropy measures, trace, etc. [[Projects:DTINoiseStatistics|More...]]

'''New: ''' Goodlett C, Fletcher P, Lin W, Gerig G. [http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=1074 Quantification of Measurement Error in DTI: Theoretical Predictions and Validation.] Proceedings of the 10th International Conference on Medical Image Computing and Computer Assisted Intervention, MICCAI 2007, LNCS 4791, pp. 10–17, 2007.

== [[Projects:DicomToNrrdForDTI|Notes on the dicom conversion for DTI data]] ==

Report about some observation when converting DTI data from dicom to dwi volumes
[[Projects:DicomToNrrdForDTI|More...]]

|}

=== Validation ===

[[Image:Cingulum1.jpg|200px]]

== [[ProjectWeek200706:ContrastingTractographyMeasures|Contrasting Tractography Measures]] ==

This project represents a new initiative to build upon a shared vision among Cores 1, 3 and 5 that the field of medical image analysis would be well served by work in the area of validation, calibration and assessment of reliability in DW-MRI image analysis. [[ProjectWeek200706:ContrastingTractographyMeasures|More...]]

'''New: ''' [[SanteFe.Tractography.Conference|Contrasting Tractography Methods Conference]], Santa Fe, October 1-2, 2007.

{| cellpadding="10"
| style="width:15%" | [[Image:MBIRNseedROIcc1.png|200px]]
| style="width:85%" |

== [[Projects:DTIValidation|DTI Validation]] ==

To carry out quantitative and qualitative validation of the DTI tractography tools. These will be applied to a limited set of specific tracts in single data sets and single tractography tools, and on several data sets using at least two tractography programs and by investigators in different laboratories. [[Projects:DTIValidation|More...]]

 Future research is needed to establish critical values for diffusion sequence acquisition parameters that would allow diffusion data processing via Slicer.

|}

NA-MIC Internal Collaborations:DiffusionImageAnalysis

2008-04-25T21:47:58Z

Sgouttard:

Back to [[NA-MIC_Internal_Collaborations|NA-MIC Internal Collaborations]]
__NOTOC__
= Diffusion Image Analysis =

=== Tractography Methods ===

{| cellpadding="10"
| style="width:15%" | [[Image:ZoomedResultWithModel.png|200px]]
| style="width:85%" |

== [[Projects:GeodesicTractographySegmentation|Geodesic Tractography Segmentation]] ==

In this work, we provide an energy minimization framework which allows one to find fiber tracts and volumetric fiber bundles in brain diffusion-weighted MRI (DW-MRI). [[Projects:GeodesicTractographySegmentation|More...]]

'''New: ''' J. Melonakos, E. Pichon, S. Angenet, and A. Tannenbaum. Finsler Active Contours. IEEE Transactions on Pattern Analysis and Machine Intelligence, 2007.

|-

| | [[Image:NAMIC callosum tracts prelim.jpg|200px]]
| |

== [[Projects:CorpusCallosumFiberTractography|Corpus Callosum Fiber Tractography]] ==

The goal of this project is to examine the integrity of fibers in the corpus callosum in patients with schizophrenia and determine whether this is associated with brain activation during memory tasks. [[Projects:CorpusCallosumFiberTractography|More...]]

'''New: ''' Wang P, Saykin A, Flashman L, Wishart H, Rabin L, Santulli R, McHugh T, MacDonald J, Mamourian A. [http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=1133 Regionally specific atrophy of the corpus callosum in AD, MCI and cognitive complaints.] Neurobiol Aging. 2006 Nov;27(11):1613-7.

|-

| | [[Image:MIT_DTI_JointSegReg_atlas3D.jpg|200px]]
| |

== [[Projects:DTIFiberRegistration|Joint Registration and Segmentation of DWI Fiber Tractography]] ==

The goal of this work is to jointly register and cluster DWI fiber tracts obtained from a group of subjects. [[Projects:DTIFiberRegistration|More...]]

'''New:''' Ziyan U, Sabuncu M, Grimson W, Westin C. [http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=1137 A Robust Algorithm for Fiber-Bundle Atlas Construction.] In Mathematical Methods in Biomedical Image Analysis (MMBIA 2007): 2007 IEEE Workshop, ICCV 2007 workshop. Rio de Janeiro, Brazil, 2007.

|-

| | [[Image:FiberTracts-angle.jpg|200px]]
| |

== [[Projects:DTIVolumetricWhiteMatterConnectivity|DTI Volumetric White Matter Connectivity]] ==

We have developed a PDE-based approach to white matter connectivity from DTI that is founded on the principal of minimal paths through the tensor volume. Our method computes a volumetric representation of a white matter tract given two endpoint regions. We have also developed statistical methods for quantifying the full tensor data along these pathways, which should be useful in clinical studies using DT-MRI. [[Projects:DTIVolumetricWhiteMatterConnectivity|More...]]

'''New: ''' Fletcher P, Tao R, Jeong W, Whitaker R. [http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=634 A volumetric approach to quantifying region-to-region white matter connectivity in diffusion tensor MRI.] Inf Process Med Imaging. 2007;20:346-358.

|-

| | [[Image:ConnectivityMap.png|200px]]
| |

== [[Projects:DTIStochasticTractography|Stochastic Tractography]] ==

This work calculates posterior distributions of white matter fiber tract parameters given diffusion observations in a DWI volume. [[Projects:DTIStochasticTractography|More...]]

|}

=== Clustering and Quantitative Analysis ===

{| cellpadding="10"
| style="width:15%" | [[Image:DTIQuantitativeAnalysis.png|200px]]
| style="width:85%" |

== [[Projects:DTIQuantitativeTractAnalysis|Quantitative Analysis of Fiber Tract Bundles]] ==

DT-MRI tractography can be used as a coordinate system for computing statistics of diffusion tensor data. The quantitative analysis of diffusion tensors takes into account the space of tensor measurements using a nonlinear Riemannian symmetric space framework. Tracts of interest are represented as a medial spline attributed with cross-sectional statistics. [[Projects:DTIQuantitativeTractAnalysis|More...]]

'''New: ''' Gilmore J, Lin W, Corouge I, Vetsa Y, Smith J, Kang C, Gu H, Hamer R, Lieberman J, Gerig G. [http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=905 Early Postnatal Development of Corpus Callosum and Corticospinal White Matter Assessed with Quantitative Tractography.] AJNR Am J Neuroradiol. 2007 Oct;28(9):1789-95.

|-

| | [[Image:CingulumAllSubjectsFibers.png|200px]]
| |

== [[Projects:DTIClustering|DTI Fiber Clustering and Fiber-Based Analysis]] ==

The goal of this project is to provide structural description of the white matter architecture as a partition into coherent fiber bundles and clusters, and to use these bundles for quantitative measurement. [[Projects:DTIClustering|More...]]

'''New:''' Monica E. Lemmond, Lauren J. O'Donnell, Stephen Whalen, Alexandra J. Golby. Characterizing Diffusion Along White Matter Tracts Affected by Primary Brain Tumors. Accepted to HBM 2007.

|-

| | [[Image:Models.jpg|200px]]
| |

== [[Projects:DTIModeling|Fiber Tract Modeling, Clustering, and Quantitative Analysis]] ==

The goal of this work is to model the shape of the fiber bundles and use this model discription in clustering and statistical analysis of fiber tracts. [[Projects:DTIModeling|More...]]

'''New:'''
M. Maddah, W. E. L. Grimson, S. K. Warfield, W. M. Wells, A Unified Framework for Clustering and Quantitative Analysis of White Matter Fiber Tracts. Medical Image Analysis, in press.

Maddah M, Wells W, Warfield S, Westin C, Grimson W. [http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=491 Probabilistic clustering and quantitative analysis of white matter fiber tracts.] Inf Process Med Imaging. 2007;20:372-83.

|-

| | [[Image:NAMIC UncinateFasiculus prelim.jpg|200px]]
| |

== [[Projects:FractionalAnisotrophyInTheUncinateFasciculus|Fractional Anisotropy in the Uncinate Fasciculus]] ==

Our objective is to measure the FA in the uncinate fasciculus in patients with schizophrenia. This project is based on the methods published by Kubicki et al. and extends that work by including a bipolar disorder control group, and determining whether there is an association between FA and cognitive functioning and symptoms in the patient groups. [[Projects:FractionalAnisotrophyInTheUncinateFasciculus|More...]]

'''New: ''' AHM 2007: Training on fiber tractography in Slicer with Sylvain Bouix that we can apply to this project as well as investigation of other fiber tracts such as the cingulate bundle.

|}

=== Other Diffusion Image Algorithms ===

{| cellpadding="10"
| style="width:15%" | [[Image:DartmouthPathOfInterest.png|200px]]
| style="width:85%" |

== [[Projects:IntegrityOfFrontoTemporalCircuitry|Integrity of Fronto-Temporal Circuitry]] ==

Our objective is to develop methodology that will permit investigators to specify functional MRI regional of interests (fROI) and determine the optimal white matter pathways between the fROIs based on DTI. [[Projects:IntegrityOfFrontoTemporalCircuitry|More...]]

'''New: ''' AHM 2007: John West had training session with Dennis Jen on new version of POI algorithm. Worked together to read new Dartmouth 3T Philips Data. Further work ongoing to integrate POI into Slicer 3.

|-

| | [[Image:Thalamus_algo_outline.png|200px]]
| |

== [[Projects:DTISegmentation|DTI-based Segmentation]] ==

Unlike conventional MRI, DTI provides adequate contrast to segment the thalamic nuclei, which are gray matter structures. [[Projects:DTISegmentation|More...]]

'''New:''' Ziyan U, Tuch D, Westin C. [http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=47 Segmentation of Thalamic Nuclei from DTI Using Spectral Clustering.] Proceedings of the 9th International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2006, LNCS 4191, pp. 807-814, 2006.Segmentation of Thalamic Nuclei from DTI using Spectral Clustering. Accepted to MICCAI 2006.

|-

| | [[Image:DTINoiseStatistics.png|200px]]
| |

== [[Projects:DTINoiseStatistics|Influence of Imaging Noise on DTI Statistics]] ==

Clinical acquisition of diffusion weighted images with high signal to noise ratio remains a challenge. The goal of this project is to understand the impact of MR noise on quantiative statistics of diffusion properties such as anisotropy measures, trace, etc. [[Projects:DTINoiseStatistics|More...]]

'''New: ''' Goodlett C, Fletcher P, Lin W, Gerig G. [http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=1074 Quantification of Measurement Error in DTI: Theoretical Predictions and Validation.] Proceedings of the 10th International Conference on Medical Image Computing and Computer Assisted Intervention, MICCAI 2007, LNCS 4791, pp. 10–17, 2007.

|}

== [[Projects:DicomToNrrdForDTI|Notes on the dicom conversion for DTI data]] ==

Report about some observation when converting DTI data from dicom to dwi volumes
[[Projects:DicomToNrrdForDTI|More...]]

|}

=== Validation ===

[[Image:Cingulum1.jpg|200px]]

== [[ProjectWeek200706:ContrastingTractographyMeasures|Contrasting Tractography Measures]] ==

This project represents a new initiative to build upon a shared vision among Cores 1, 3 and 5 that the field of medical image analysis would be well served by work in the area of validation, calibration and assessment of reliability in DW-MRI image analysis. [[ProjectWeek200706:ContrastingTractographyMeasures|More...]]

'''New: ''' [[SanteFe.Tractography.Conference|Contrasting Tractography Methods Conference]], Santa Fe, October 1-2, 2007.

{| cellpadding="10"
| style="width:15%" | [[Image:MBIRNseedROIcc1.png|200px]]
| style="width:85%" |

== [[Projects:DTIValidation|DTI Validation]] ==

To carry out quantitative and qualitative validation of the DTI tractography tools. These will be applied to a limited set of specific tracts in single data sets and single tractography tools, and on several data sets using at least two tractography programs and by investigators in different laboratories. [[Projects:DTIValidation|More...]]

 Future research is needed to establish critical values for diffusion sequence acquisition parameters that would allow diffusion data processing via Slicer.

|}

NA-MIC Internal Collaborations:DiffusionImageAnalysis

2008-04-25T21:47:16Z

Sgouttard:

Back to [[NA-MIC_Internal_Collaborations|NA-MIC Internal Collaborations]]
__NOTOC__
= Diffusion Image Analysis =

=== Tractography Methods ===

{| cellpadding="10"
| style="width:15%" | [[Image:ZoomedResultWithModel.png|200px]]
| style="width:85%" |

== [[Projects:GeodesicTractographySegmentation|Geodesic Tractography Segmentation]] ==

In this work, we provide an energy minimization framework which allows one to find fiber tracts and volumetric fiber bundles in brain diffusion-weighted MRI (DW-MRI). [[Projects:GeodesicTractographySegmentation|More...]]

'''New: ''' J. Melonakos, E. Pichon, S. Angenet, and A. Tannenbaum. Finsler Active Contours. IEEE Transactions on Pattern Analysis and Machine Intelligence, 2007.

|-

| | [[Image:NAMIC callosum tracts prelim.jpg|200px]]
| |

== [[Projects:CorpusCallosumFiberTractography|Corpus Callosum Fiber Tractography]] ==

The goal of this project is to examine the integrity of fibers in the corpus callosum in patients with schizophrenia and determine whether this is associated with brain activation during memory tasks. [[Projects:CorpusCallosumFiberTractography|More...]]

'''New: ''' Wang P, Saykin A, Flashman L, Wishart H, Rabin L, Santulli R, McHugh T, MacDonald J, Mamourian A. [http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=1133 Regionally specific atrophy of the corpus callosum in AD, MCI and cognitive complaints.] Neurobiol Aging. 2006 Nov;27(11):1613-7.

|-

| | [[Image:MIT_DTI_JointSegReg_atlas3D.jpg|200px]]
| |

== [[Projects:DTIFiberRegistration|Joint Registration and Segmentation of DWI Fiber Tractography]] ==

The goal of this work is to jointly register and cluster DWI fiber tracts obtained from a group of subjects. [[Projects:DTIFiberRegistration|More...]]

'''New:''' Ziyan U, Sabuncu M, Grimson W, Westin C. [http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=1137 A Robust Algorithm for Fiber-Bundle Atlas Construction.] In Mathematical Methods in Biomedical Image Analysis (MMBIA 2007): 2007 IEEE Workshop, ICCV 2007 workshop. Rio de Janeiro, Brazil, 2007.

|-

| | [[Image:FiberTracts-angle.jpg|200px]]
| |

== [[Projects:DTIVolumetricWhiteMatterConnectivity|DTI Volumetric White Matter Connectivity]] ==

We have developed a PDE-based approach to white matter connectivity from DTI that is founded on the principal of minimal paths through the tensor volume. Our method computes a volumetric representation of a white matter tract given two endpoint regions. We have also developed statistical methods for quantifying the full tensor data along these pathways, which should be useful in clinical studies using DT-MRI. [[Projects:DTIVolumetricWhiteMatterConnectivity|More...]]

'''New: ''' Fletcher P, Tao R, Jeong W, Whitaker R. [http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=634 A volumetric approach to quantifying region-to-region white matter connectivity in diffusion tensor MRI.] Inf Process Med Imaging. 2007;20:346-358.

|-

| | [[Image:ConnectivityMap.png|200px]]
| |

== [[Projects:DTIStochasticTractography|Stochastic Tractography]] ==

This work calculates posterior distributions of white matter fiber tract parameters given diffusion observations in a DWI volume. [[Projects:DTIStochasticTractography|More...]]

|}

=== Clustering and Quantitative Analysis ===

{| cellpadding="10"
| style="width:15%" | [[Image:DTIQuantitativeAnalysis.png|200px]]
| style="width:85%" |

== [[Projects:DTIQuantitativeTractAnalysis|Quantitative Analysis of Fiber Tract Bundles]] ==

DT-MRI tractography can be used as a coordinate system for computing statistics of diffusion tensor data. The quantitative analysis of diffusion tensors takes into account the space of tensor measurements using a nonlinear Riemannian symmetric space framework. Tracts of interest are represented as a medial spline attributed with cross-sectional statistics. [[Projects:DTIQuantitativeTractAnalysis|More...]]

'''New: ''' Gilmore J, Lin W, Corouge I, Vetsa Y, Smith J, Kang C, Gu H, Hamer R, Lieberman J, Gerig G. [http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=905 Early Postnatal Development of Corpus Callosum and Corticospinal White Matter Assessed with Quantitative Tractography.] AJNR Am J Neuroradiol. 2007 Oct;28(9):1789-95.

|-

| | [[Image:CingulumAllSubjectsFibers.png|200px]]
| |

== [[Projects:DTIClustering|DTI Fiber Clustering and Fiber-Based Analysis]] ==

The goal of this project is to provide structural description of the white matter architecture as a partition into coherent fiber bundles and clusters, and to use these bundles for quantitative measurement. [[Projects:DTIClustering|More...]]

'''New:''' Monica E. Lemmond, Lauren J. O'Donnell, Stephen Whalen, Alexandra J. Golby. Characterizing Diffusion Along White Matter Tracts Affected by Primary Brain Tumors. Accepted to HBM 2007.

|-

| | [[Image:Models.jpg|200px]]
| |

== [[Projects:DTIModeling|Fiber Tract Modeling, Clustering, and Quantitative Analysis]] ==

The goal of this work is to model the shape of the fiber bundles and use this model discription in clustering and statistical analysis of fiber tracts. [[Projects:DTIModeling|More...]]

'''New:'''
M. Maddah, W. E. L. Grimson, S. K. Warfield, W. M. Wells, A Unified Framework for Clustering and Quantitative Analysis of White Matter Fiber Tracts. Medical Image Analysis, in press.

Maddah M, Wells W, Warfield S, Westin C, Grimson W. [http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=491 Probabilistic clustering and quantitative analysis of white matter fiber tracts.] Inf Process Med Imaging. 2007;20:372-83.

|-

| | [[Image:NAMIC UncinateFasiculus prelim.jpg|200px]]
| |

== [[Projects:FractionalAnisotrophyInTheUncinateFasciculus|Fractional Anisotropy in the Uncinate Fasciculus]] ==

Our objective is to measure the FA in the uncinate fasciculus in patients with schizophrenia. This project is based on the methods published by Kubicki et al. and extends that work by including a bipolar disorder control group, and determining whether there is an association between FA and cognitive functioning and symptoms in the patient groups. [[Projects:FractionalAnisotrophyInTheUncinateFasciculus|More...]]

'''New: ''' AHM 2007: Training on fiber tractography in Slicer with Sylvain Bouix that we can apply to this project as well as investigation of other fiber tracts such as the cingulate bundle.

|}

=== Other Diffusion Image Algorithms ===

{| cellpadding="10"
| style="width:15%" | [[Image:DartmouthPathOfInterest.png|200px]]
| style="width:85%" |

== [[Projects:IntegrityOfFrontoTemporalCircuitry|Integrity of Fronto-Temporal Circuitry]] ==

Our objective is to develop methodology that will permit investigators to specify functional MRI regional of interests (fROI) and determine the optimal white matter pathways between the fROIs based on DTI. [[Projects:IntegrityOfFrontoTemporalCircuitry|More...]]

'''New: ''' AHM 2007: John West had training session with Dennis Jen on new version of POI algorithm. Worked together to read new Dartmouth 3T Philips Data. Further work ongoing to integrate POI into Slicer 3.

|-

| | [[Image:Thalamus_algo_outline.png|200px]]
| |

== [[Projects:DTISegmentation|DTI-based Segmentation]] ==

Unlike conventional MRI, DTI provides adequate contrast to segment the thalamic nuclei, which are gray matter structures. [[Projects:DTISegmentation|More...]]

'''New:''' Ziyan U, Tuch D, Westin C. [http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=47 Segmentation of Thalamic Nuclei from DTI Using Spectral Clustering.] Proceedings of the 9th International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2006, LNCS 4191, pp. 807-814, 2006.Segmentation of Thalamic Nuclei from DTI using Spectral Clustering. Accepted to MICCAI 2006.

|-

| | [[Image:DTINoiseStatistics.png|200px]]
| |

== [[Projects:DTINoiseStatistics|Influence of Imaging Noise on DTI Statistics]] ==

Clinical acquisition of diffusion weighted images with high signal to noise ratio remains a challenge. The goal of this project is to understand the impact of MR noise on quantiative statistics of diffusion properties such as anisotropy measures, trace, etc. [[Projects:DTINoiseStatistics|More...]]

'''New: ''' Goodlett C, Fletcher P, Lin W, Gerig G. [http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=1074 Quantification of Measurement Error in DTI: Theoretical Predictions and Validation.] Proceedings of the 10th International Conference on Medical Image Computing and Computer Assisted Intervention, MICCAI 2007, LNCS 4791, pp. 10–17, 2007.

|}

| | [[Image:ScannerToFib.png|200px]]
| |

== [[Projects:DicomToNrrdForDTI|Notes on the dicom conversion for DTI data]] ==

Report about some observation when converting DTI data from dicom to dwi volumes
[[Projects:DicomToNrrdForDTI|More...]]

|}

=== Validation ===

[[Image:Cingulum1.jpg|200px]]

== [[ProjectWeek200706:ContrastingTractographyMeasures|Contrasting Tractography Measures]] ==

This project represents a new initiative to build upon a shared vision among Cores 1, 3 and 5 that the field of medical image analysis would be well served by work in the area of validation, calibration and assessment of reliability in DW-MRI image analysis. [[ProjectWeek200706:ContrastingTractographyMeasures|More...]]

'''New: ''' [[SanteFe.Tractography.Conference|Contrasting Tractography Methods Conference]], Santa Fe, October 1-2, 2007.

{| cellpadding="10"
| style="width:15%" | [[Image:MBIRNseedROIcc1.png|200px]]
| style="width:85%" |

== [[Projects:DTIValidation|DTI Validation]] ==

To carry out quantitative and qualitative validation of the DTI tractography tools. These will be applied to a limited set of specific tracts in single data sets and single tractography tools, and on several data sets using at least two tractography programs and by investigators in different laboratories. [[Projects:DTIValidation|More...]]

 Future research is needed to establish critical values for diffusion sequence acquisition parameters that would allow diffusion data processing via Slicer.

|}

File:ScannerToFib.png

2008-04-25T21:46:32Z

Sgouttard:

Projects:DicomToNrrdForDTI

2008-04-25T21:26:34Z

Sgouttard: New page: Dicom conversion for DTI data Here are a few notes about our observations on the conversion of DTI dicom data from a TimTrio scanner to volumes

Dicom conversion for DTI data

Here are a few notes about our observations on the conversion of DTI dicom data from a TimTrio scanner to volumes

NA-MIC Internal Collaborations:DiffusionImageAnalysis

2008-04-25T21:18:20Z

Sgouttard:

Back to [[NA-MIC_Internal_Collaborations|NA-MIC Internal Collaborations]]
__NOTOC__
= Diffusion Image Analysis =

=== Tractography Methods ===

{| cellpadding="10"
| style="width:15%" | [[Image:ZoomedResultWithModel.png|200px]]
| style="width:85%" |

== [[Projects:GeodesicTractographySegmentation|Geodesic Tractography Segmentation]] ==

In this work, we provide an energy minimization framework which allows one to find fiber tracts and volumetric fiber bundles in brain diffusion-weighted MRI (DW-MRI). [[Projects:GeodesicTractographySegmentation|More...]]

'''New: ''' J. Melonakos, E. Pichon, S. Angenet, and A. Tannenbaum. Finsler Active Contours. IEEE Transactions on Pattern Analysis and Machine Intelligence, 2007.

|-

| | [[Image:NAMIC callosum tracts prelim.jpg|200px]]
| |

== [[Projects:CorpusCallosumFiberTractography|Corpus Callosum Fiber Tractography]] ==

The goal of this project is to examine the integrity of fibers in the corpus callosum in patients with schizophrenia and determine whether this is associated with brain activation during memory tasks. [[Projects:CorpusCallosumFiberTractography|More...]]

'''New: ''' Wang P, Saykin A, Flashman L, Wishart H, Rabin L, Santulli R, McHugh T, MacDonald J, Mamourian A. [http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=1133 Regionally specific atrophy of the corpus callosum in AD, MCI and cognitive complaints.] Neurobiol Aging. 2006 Nov;27(11):1613-7.

|-

| | [[Image:MIT_DTI_JointSegReg_atlas3D.jpg|200px]]
| |

== [[Projects:DTIFiberRegistration|Joint Registration and Segmentation of DWI Fiber Tractography]] ==

The goal of this work is to jointly register and cluster DWI fiber tracts obtained from a group of subjects. [[Projects:DTIFiberRegistration|More...]]

'''New:''' Ziyan U, Sabuncu M, Grimson W, Westin C. [http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=1137 A Robust Algorithm for Fiber-Bundle Atlas Construction.] In Mathematical Methods in Biomedical Image Analysis (MMBIA 2007): 2007 IEEE Workshop, ICCV 2007 workshop. Rio de Janeiro, Brazil, 2007.

|-

| | [[Image:FiberTracts-angle.jpg|200px]]
| |

== [[Projects:DTIVolumetricWhiteMatterConnectivity|DTI Volumetric White Matter Connectivity]] ==

We have developed a PDE-based approach to white matter connectivity from DTI that is founded on the principal of minimal paths through the tensor volume. Our method computes a volumetric representation of a white matter tract given two endpoint regions. We have also developed statistical methods for quantifying the full tensor data along these pathways, which should be useful in clinical studies using DT-MRI. [[Projects:DTIVolumetricWhiteMatterConnectivity|More...]]

'''New: ''' Fletcher P, Tao R, Jeong W, Whitaker R. [http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=634 A volumetric approach to quantifying region-to-region white matter connectivity in diffusion tensor MRI.] Inf Process Med Imaging. 2007;20:346-358.

|-

| | [[Image:ConnectivityMap.png|200px]]
| |

== [[Projects:DTIStochasticTractography|Stochastic Tractography]] ==

This work calculates posterior distributions of white matter fiber tract parameters given diffusion observations in a DWI volume. [[Projects:DTIStochasticTractography|More...]]

|}

=== Clustering and Quantitative Analysis ===

{| cellpadding="10"
| style="width:15%" | [[Image:DTIQuantitativeAnalysis.png|200px]]
| style="width:85%" |

== [[Projects:DTIQuantitativeTractAnalysis|Quantitative Analysis of Fiber Tract Bundles]] ==

DT-MRI tractography can be used as a coordinate system for computing statistics of diffusion tensor data. The quantitative analysis of diffusion tensors takes into account the space of tensor measurements using a nonlinear Riemannian symmetric space framework. Tracts of interest are represented as a medial spline attributed with cross-sectional statistics. [[Projects:DTIQuantitativeTractAnalysis|More...]]

'''New: ''' Gilmore J, Lin W, Corouge I, Vetsa Y, Smith J, Kang C, Gu H, Hamer R, Lieberman J, Gerig G. [http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=905 Early Postnatal Development of Corpus Callosum and Corticospinal White Matter Assessed with Quantitative Tractography.] AJNR Am J Neuroradiol. 2007 Oct;28(9):1789-95.

|-

| | [[Image:CingulumAllSubjectsFibers.png|200px]]
| |

== [[Projects:DTIClustering|DTI Fiber Clustering and Fiber-Based Analysis]] ==

The goal of this project is to provide structural description of the white matter architecture as a partition into coherent fiber bundles and clusters, and to use these bundles for quantitative measurement. [[Projects:DTIClustering|More...]]

'''New:''' Monica E. Lemmond, Lauren J. O'Donnell, Stephen Whalen, Alexandra J. Golby. Characterizing Diffusion Along White Matter Tracts Affected by Primary Brain Tumors. Accepted to HBM 2007.

|-

| | [[Image:Models.jpg|200px]]
| |

== [[Projects:DTIModeling|Fiber Tract Modeling, Clustering, and Quantitative Analysis]] ==

The goal of this work is to model the shape of the fiber bundles and use this model discription in clustering and statistical analysis of fiber tracts. [[Projects:DTIModeling|More...]]

'''New:'''
M. Maddah, W. E. L. Grimson, S. K. Warfield, W. M. Wells, A Unified Framework for Clustering and Quantitative Analysis of White Matter Fiber Tracts. Medical Image Analysis, in press.

Maddah M, Wells W, Warfield S, Westin C, Grimson W. [http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=491 Probabilistic clustering and quantitative analysis of white matter fiber tracts.] Inf Process Med Imaging. 2007;20:372-83.

|-

| | [[Image:NAMIC UncinateFasiculus prelim.jpg|200px]]
| |

== [[Projects:FractionalAnisotrophyInTheUncinateFasciculus|Fractional Anisotropy in the Uncinate Fasciculus]] ==

Our objective is to measure the FA in the uncinate fasciculus in patients with schizophrenia. This project is based on the methods published by Kubicki et al. and extends that work by including a bipolar disorder control group, and determining whether there is an association between FA and cognitive functioning and symptoms in the patient groups. [[Projects:FractionalAnisotrophyInTheUncinateFasciculus|More...]]

'''New: ''' AHM 2007: Training on fiber tractography in Slicer with Sylvain Bouix that we can apply to this project as well as investigation of other fiber tracts such as the cingulate bundle.

|}

=== Other Diffusion Image Algorithms ===

{| cellpadding="10"
| style="width:15%" | [[Image:DartmouthPathOfInterest.png|200px]]
| style="width:85%" |

== [[Projects:IntegrityOfFrontoTemporalCircuitry|Integrity of Fronto-Temporal Circuitry]] ==

Our objective is to develop methodology that will permit investigators to specify functional MRI regional of interests (fROI) and determine the optimal white matter pathways between the fROIs based on DTI. [[Projects:IntegrityOfFrontoTemporalCircuitry|More...]]

'''New: ''' AHM 2007: John West had training session with Dennis Jen on new version of POI algorithm. Worked together to read new Dartmouth 3T Philips Data. Further work ongoing to integrate POI into Slicer 3.

|-

| | [[Image:Thalamus_algo_outline.png|200px]]
| |

== [[Projects:DTISegmentation|DTI-based Segmentation]] ==

Unlike conventional MRI, DTI provides adequate contrast to segment the thalamic nuclei, which are gray matter structures. [[Projects:DTISegmentation|More...]]

'''New:''' Ziyan U, Tuch D, Westin C. [http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=47 Segmentation of Thalamic Nuclei from DTI Using Spectral Clustering.] Proceedings of the 9th International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2006, LNCS 4191, pp. 807-814, 2006.Segmentation of Thalamic Nuclei from DTI using Spectral Clustering. Accepted to MICCAI 2006.

|-

| | [[Image:DTINoiseStatistics.png|200px]]
| |

== [[Projects:DTINoiseStatistics|Influence of Imaging Noise on DTI Statistics]] ==

Clinical acquisition of diffusion weighted images with high signal to noise ratio remains a challenge. The goal of this project is to understand the impact of MR noise on quantiative statistics of diffusion properties such as anisotropy measures, trace, etc. [[Projects:DTINoiseStatistics|More...]]

'''New: ''' Goodlett C, Fletcher P, Lin W, Gerig G. [http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=1074 Quantification of Measurement Error in DTI: Theoretical Predictions and Validation.] Proceedings of the 10th International Conference on Medical Image Computing and Computer Assisted Intervention, MICCAI 2007, LNCS 4791, pp. 10–17, 2007.

|}

| | [[Image:DicomToNrrdForDTI.png|200px]]
| |

== [[Projects:DicomToNrrdForDTI|Notes on the dicom conversion for DTI data]] ==

Report about some observation when converting DTI data from dicom to dwi volumes
[[Projects:DicomToNrrdForDTI|More...]]

|}

=== Validation ===

[[Image:Cingulum1.jpg|200px]]

== [[ProjectWeek200706:ContrastingTractographyMeasures|Contrasting Tractography Measures]] ==

This project represents a new initiative to build upon a shared vision among Cores 1, 3 and 5 that the field of medical image analysis would be well served by work in the area of validation, calibration and assessment of reliability in DW-MRI image analysis. [[ProjectWeek200706:ContrastingTractographyMeasures|More...]]

'''New: ''' [[SanteFe.Tractography.Conference|Contrasting Tractography Methods Conference]], Santa Fe, October 1-2, 2007.

{| cellpadding="10"
| style="width:15%" | [[Image:MBIRNseedROIcc1.png|200px]]
| style="width:85%" |

== [[Projects:DTIValidation|DTI Validation]] ==

To carry out quantitative and qualitative validation of the DTI tractography tools. These will be applied to a limited set of specific tracts in single data sets and single tractography tools, and on several data sets using at least two tractography programs and by investigators in different laboratories. [[Projects:DTIValidation|More...]]

 Future research is needed to establish critical values for diffusion sequence acquisition parameters that would allow diffusion data processing via Slicer.

|}

File:DTIphantom tensorfield screenshot.png

2008-02-04T23:22:25Z

Sgouttard:

SanteFe.Tractography.Conference

2007-09-28T18:48:22Z

Sgouttard:

= Goals =
We in NA-MIC, and our collaborating colleagues from BIRN, NAC and UIowa, are in a unique position to make a substanital contribution to the field of knowledge concerning the validation of medical image processing of Diffusion Tensor Image data. Among our faculty are leaders in the field of not only DTI analysis algorithm development, but also of validation and calibration. We seek to use our unique opportunity for multi-site collaboration to advance knowledge in this area for the benefit of clinical and computational scientists.

* To compare and contrast the results of tractography algorithms included in or supported by the NA-MIC Toolkit on a benchmark dataset of Diffusion Tensor Imaging (DTI) data. 
* To develop a framework for systematically and statistically comparing and contrasting these outcome measures mapped to specific manuscript preparation. 
* To map out appropriate leadership for each of the proposed manuscripts. 
* To initiate development of tutorials for tractography algorithms not yet in the NAMIC Training Compendium. 
* To propose methods for NA-MIC benchmarks of calibration and validation of tractography algorithms for further discussion at the 2008 AHM. 

== Conference Logistics ==

* October 1-2, 2007, 8:00 AM- 6:00 PM 
* The workshop is being held in the Governors Room at the Inn of the Governors, 101 W. Alameda, Sante Fe, NM 87501, 1-800-234-4534, http://www.innofthegovernors.com/ 
* We have booked a block of rooms for $169.00/night for single or double occupancy September 30- October 3, 2007 (Sunday through Tuesday nights). Our reservation code is "NAMIC" and the deadline for reservations is August 31, 2007. The price includes a full breakfast buffet, wireless internet access in the lobby, meeting room and sleeping rooms at no additional cost. 
* Fly into Albuquerque, NM. Information about shuttles from the airport to the hotel can be found here http://www.sandiashuttle.com/.

Many grateful thanks to John Rasure and Debbie Lynch of the MIND Institute for their assistance in making these arrangements.

==Registration==
* '''To register, add your name to the list of attendees below and make your flight and hotel reservations'''

* Questions about logistics and the content of the Conference should be addressed to Randy Gollub (rgollub at partners.org).

* '''This Conference is supported by the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on the National Centers for Biomedical Computing can be obtained from http://nihroadmap.nih.gov/bioinformatics'''.

== Conference Attendees ==

# Ross Whitaker, PhD
# Guido Gerig, PhD, Utah
# Casey Goodlett, Utah
# Carl-Fredrik Westin, PhD
# Marek Kubicki, MD, PhD
# Sylvain Bouix, PNL
# [[User:Randy|Randy Gollub, MD, PhD]], Harvard Medical School (Department of Psychiatry and Martinos Center, Department of Radiology, Massachussets General Hospital)
# [[User:SPujol|Sonia Pujol, PhD]], Harvard Medical School (Surgical Planning Laboratory, Department of Radiology, Brigham and Women's Hospital)
# H. Jeremy Bockholt, The MIND Institute
# [[User:Melonakos|John Melonakos]], Georgia Tech
# [[User:Kikinis|Ron Kikinis, MD]], SPL
# Tom Fletcher, Utah
# Anastasia Yendiki, MGH
# Allen Song, PhD Duke
# Tri Ngo, BWH
# Marc Niethammer, BWH
# Lauren O'Donnell, BWH
# Vincent Magnotta, Iowa
# Sylvain Gouttard, Utah
 

== Preparation for Workshop -- ''Important Information for all attendees'' ==

Suggestions: [[July31T-con |Notes from July 31 Planning T-con with detailed "To Dos"]]

Suggested background reading for workshop: 

#[[Media:AHM2006-validation-DTI-gg.ppt| Guido's 2006 AHM presentation on Validation strategies for DTI analysis]]
#[[Media:DWI.reproducibility.pdf]]
#[[http://cds.ismrm.org/protected/DiffusionWorkshop05 If any of you attended the 2005 ISMRM Workshop on Methods for Quantitative Diffusion of MRI of Human Brain and can get us access to the detailed summary, I have seen it and it might be very useful]]
#Presentations by and Fitzpatrick from the [http://idm.univ-rennes1.fr/VMIP/miccai2003/presentations.html MICCAI 2003 Tutorial on Validation in Medical Image Processing]
#Peruse the webpages associated with the [http://www.vuse.vanderbilt.edu/~image/registration/ Retrospective Image Registration Evaluation project]
#[http://ieeexplore.ieee.org/Xplore/login.jsp?url=/iel5/10818/34114/01624925.pdf anyone have access to this?]
#[[Media:BrainTissueClassifiers_BouixNeuroimage2007.pdf| Sylvain's segmentation comparison manuscript]]
#[[Media:MonkeyDTIStudy_Neuroimage2007.pdf| CF Westin's experimental study manuscript]]

Please complete the following items prior to the workshop.
'''This is hands-on Conference. All participants must come with their own computer loaded with the calibration data and the results of their own algorithm analysis. ''' 

'''Benchmark Datasets'''

== Agenda ==

== Welcome to Santa Fe Dinner ==

Sunday September 30th, 7:45 PM
La Casa Sena, 125 E. Palace, 505-988-9232 (www.lacasasena.com)

=== '''October 1, Meeting 8:30 AM - 6 PM''' ===
* 7:30- 8:30 AM Enjoy the breakfast buffet at the hotel
* 8:30 - 8:40 AM '''Goals of Conference''' Randy Gollub
* 8:40 - 11:45 AM '''Presentations of results from each of the participants & discussion:''' Guidelines: Please use this [[Media:NAMIC_Tractography_Conference_template.ppt| presentation template]].‎
Report-style, no details of methods known from previous Core-1 meetings, report about processing steps, parameters, user-interaction, user time, structure of results. Summary of difficulties and obstacles
**8:40 Guido Gerig set stage for series of presentations focusing on [http://www.na-mic.org/Wiki/index.php/Projects/Diffusion/Contrasting_Tractography_Measures tractography methods] and results
**8:50 Marek Kubicki Clinical Description of Fiber Bundles and Regions of Interest
**Session 1: 9:10-10:30
***9:10 Sonia Pujol (BWH) Streamline Tractography in Slicer using ROI and Whole Brain Seeding
***9:40 Sylvain Gouttard (Utah) FiberViewer
***10:05 Tri Ngo (BWH) Stochastic Tractography
** 10:30 -10:45 Coffee Break (place lunch order)
**Session 2: 10:45-12:30
***10:45 John Melonakos (GA) Geodesic Active Contours
***11:10 Ross Whitaker/Tom Fletcher (Utah) Volumetric Connectivity
***11:35 Casey Goodlett (Utah) DTI Atlas
*12:00 Lunch
*1:00 Ross Whitaker to kick-off discussion with summarizing ideas & focus
* 1:15 - 2:15 PM '''What did we learn?'''
** Problems with data quality (noise, on-scanner up-interpolation, size of datasets, Eddy current distortion, EPI distortion, artifacts etc.
** Problems with ROI definitions, appropriateness of methods given the data.
** Data issues: NRRD header interpretation, output formats, optimal calculation of tensors, others.
* 2:15 - 6:00 PM '''Where are we going with DTI processing?'''
** Towards statistical analysis of resulting measures obtained from processing: Approaches, pitfalls (like trying to count streamlines), statistics of tensors, statistics of FA values, functional analysis, multiple comparison correction, others.
** Discuss methods and metrics for contrasting/comparing outcomes of DTI analyses.
** Set detailed agenda for Tuesday
(coffee break somewhere above)

* 7:00 PM Dinner at local restaurant(s) to be found by wandering around town

=== '''October 2, 8:30 AM - 5 PM''' ===
* 7:30- 8:30 AM Enjoy the breakfast buffet at the hotel
* 8:30 - 8:50 AM Neurosurgical applications of tractography: Lauren O'Donnell (BHW)
* 8:50 - 9:00 AM Pilot results from the MIND multi-site DTI reliability dataset: Jeremy Bockholt (UNM)
* 9:00 - 10:15 '''Discuss what to do next on this project'''
* 10:15 -10:30 Coffee Break
* 10:30 - 11:45 '''Continue to formulate a plan for next steps on this project'''
* 11:45 - 1:00 PM Lunch together at local restaurant
* 1:00 - 3:00 PM '''?'''
* 3:00 - 3:15 PM Coffee Break
* 3:15 - 5:00 PM Formulation of action plan and assignment of tasks

 

Return to [[Projects/Diffusion/2007_Project_Week_Contrasting_Tractography_Measures | Contrasting Tractography Project Page]]

SanteFe.Tractography.Conference

2007-09-28T18:47:49Z

Sgouttard:

= Goals =
We in NA-MIC, and our collaborating colleagues from BIRN, NAC and UIowa, are in a unique position to make a substanital contribution to the field of knowledge concerning the validation of medical image processing of Diffusion Tensor Image data. Among our faculty are leaders in the field of not only DTI analysis algorithm development, but also of validation and calibration. We seek to use our unique opportunity for multi-site collaboration to advance knowledge in this area for the benefit of clinical and computational scientists.

* To compare and contrast the results of tractography algorithms included in or supported by the NA-MIC Toolkit on a benchmark dataset of Diffusion Tensor Imaging (DTI) data. 
* To develop a framework for systematically and statistically comparing and contrasting these outcome measures mapped to specific manuscript preparation. 
* To map out appropriate leadership for each of the proposed manuscripts. 
* To initiate development of tutorials for tractography algorithms not yet in the NAMIC Training Compendium. 
* To propose methods for NA-MIC benchmarks of calibration and validation of tractography algorithms for further discussion at the 2008 AHM. 

== Conference Logistics ==

* October 1-2, 2007, 8:00 AM- 6:00 PM 
* The workshop is being held in the Governors Room at the Inn of the Governors, 101 W. Alameda, Sante Fe, NM 87501, 1-800-234-4534, http://www.innofthegovernors.com/ 
* We have booked a block of rooms for $169.00/night for single or double occupancy September 30- October 3, 2007 (Sunday through Tuesday nights). Our reservation code is "NAMIC" and the deadline for reservations is August 31, 2007. The price includes a full breakfast buffet, wireless internet access in the lobby, meeting room and sleeping rooms at no additional cost. 
* Fly into Albuquerque, NM. Information about shuttles from the airport to the hotel can be found here http://www.sandiashuttle.com/.

Many grateful thanks to John Rasure and Debbie Lynch of the MIND Institute for their assistance in making these arrangements.

==Registration==
* '''To register, add your name to the list of attendees below and make your flight and hotel reservations'''

* Questions about logistics and the content of the Conference should be addressed to Randy Gollub (rgollub at partners.org).

* '''This Conference is supported by the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on the National Centers for Biomedical Computing can be obtained from http://nihroadmap.nih.gov/bioinformatics'''.

== Conference Attendees ==

# Ross Whitaker, PhD
# Guido Gerig, PhD, Utah
# Casey Goodlett, Utah
# Carl-Fredrik Westin, PhD
# Marek Kubicki, MD, PhD
# Sylvain Bouix, PNL
# [[User:Randy|Randy Gollub, MD, PhD]], Harvard Medical School (Department of Psychiatry and Martinos Center, Department of Radiology, Massachussets General Hospital)
# [[User:SPujol|Sonia Pujol, PhD]], Harvard Medical School (Surgical Planning Laboratory, Department of Radiology, Brigham and Women's Hospital)
# H. Jeremy Bockholt, The MIND Institute
# [[User:Melonakos|John Melonakos]], Georgia Tech
# [[User:Kikinis|Ron Kikinis, MD]], SPL
# Tom Fletcher, Utah
# Anastasia Yendiki, MGH
# Allen Song, PhD Duke
# Tri Ngo, BWH
# Marc Niethammer, BWH
# Lauren O'Donnell, BWH
# Vincent Magnotta, Iowa
# [[Image:SantaFeTractography_Gouttard.ppt‎ | Sylvain Gouttard, Utah]]
 

== Preparation for Workshop -- ''Important Information for all attendees'' ==

Suggestions: [[July31T-con |Notes from July 31 Planning T-con with detailed "To Dos"]]

Suggested background reading for workshop: 

#[[Media:AHM2006-validation-DTI-gg.ppt| Guido's 2006 AHM presentation on Validation strategies for DTI analysis]]
#[[Media:DWI.reproducibility.pdf]]
#[[http://cds.ismrm.org/protected/DiffusionWorkshop05 If any of you attended the 2005 ISMRM Workshop on Methods for Quantitative Diffusion of MRI of Human Brain and can get us access to the detailed summary, I have seen it and it might be very useful]]
#Presentations by and Fitzpatrick from the [http://idm.univ-rennes1.fr/VMIP/miccai2003/presentations.html MICCAI 2003 Tutorial on Validation in Medical Image Processing]
#Peruse the webpages associated with the [http://www.vuse.vanderbilt.edu/~image/registration/ Retrospective Image Registration Evaluation project]
#[http://ieeexplore.ieee.org/Xplore/login.jsp?url=/iel5/10818/34114/01624925.pdf anyone have access to this?]
#[[Media:BrainTissueClassifiers_BouixNeuroimage2007.pdf| Sylvain's segmentation comparison manuscript]]
#[[Media:MonkeyDTIStudy_Neuroimage2007.pdf| CF Westin's experimental study manuscript]]

Please complete the following items prior to the workshop.
'''This is hands-on Conference. All participants must come with their own computer loaded with the calibration data and the results of their own algorithm analysis. ''' 

'''Benchmark Datasets'''

== Agenda ==

== Welcome to Santa Fe Dinner ==

Sunday September 30th, 7:45 PM
La Casa Sena, 125 E. Palace, 505-988-9232 (www.lacasasena.com)

=== '''October 1, Meeting 8:30 AM - 6 PM''' ===
* 7:30- 8:30 AM Enjoy the breakfast buffet at the hotel
* 8:30 - 8:40 AM '''Goals of Conference''' Randy Gollub
* 8:40 - 11:45 AM '''Presentations of results from each of the participants & discussion:''' Guidelines: Please use this [[Media:NAMIC_Tractography_Conference_template.ppt| presentation template]].‎
Report-style, no details of methods known from previous Core-1 meetings, report about processing steps, parameters, user-interaction, user time, structure of results. Summary of difficulties and obstacles
**8:40 Guido Gerig set stage for series of presentations focusing on [http://www.na-mic.org/Wiki/index.php/Projects/Diffusion/Contrasting_Tractography_Measures tractography methods] and results
**8:50 Marek Kubicki Clinical Description of Fiber Bundles and Regions of Interest
**Session 1: 9:10-10:30
***9:10 Sonia Pujol (BWH) Streamline Tractography in Slicer using ROI and Whole Brain Seeding
***9:40 Sylvain Gouttard (Utah) FiberViewer
***10:05 Tri Ngo (BWH) Stochastic Tractography
** 10:30 -10:45 Coffee Break (place lunch order)
**Session 2: 10:45-12:30
***10:45 John Melonakos (GA) Geodesic Active Contours
***11:10 Ross Whitaker/Tom Fletcher (Utah) Volumetric Connectivity
***11:35 Casey Goodlett (Utah) DTI Atlas
*12:00 Lunch
*1:00 Ross Whitaker to kick-off discussion with summarizing ideas & focus
* 1:15 - 2:15 PM '''What did we learn?'''
** Problems with data quality (noise, on-scanner up-interpolation, size of datasets, Eddy current distortion, EPI distortion, artifacts etc.
** Problems with ROI definitions, appropriateness of methods given the data.
** Data issues: NRRD header interpretation, output formats, optimal calculation of tensors, others.
* 2:15 - 6:00 PM '''Where are we going with DTI processing?'''
** Towards statistical analysis of resulting measures obtained from processing: Approaches, pitfalls (like trying to count streamlines), statistics of tensors, statistics of FA values, functional analysis, multiple comparison correction, others.
** Discuss methods and metrics for contrasting/comparing outcomes of DTI analyses.
** Set detailed agenda for Tuesday
(coffee break somewhere above)

* 7:00 PM Dinner at local restaurant(s) to be found by wandering around town

=== '''October 2, 8:30 AM - 5 PM''' ===
* 7:30- 8:30 AM Enjoy the breakfast buffet at the hotel
* 8:30 - 8:50 AM Neurosurgical applications of tractography: Lauren O'Donnell (BHW)
* 8:50 - 9:00 AM Pilot results from the MIND multi-site DTI reliability dataset: Jeremy Bockholt (UNM)
* 9:00 - 10:15 '''Discuss what to do next on this project'''
* 10:15 -10:30 Coffee Break
* 10:30 - 11:45 '''Continue to formulate a plan for next steps on this project'''
* 11:45 - 1:00 PM Lunch together at local restaurant
* 1:00 - 3:00 PM '''?'''
* 3:00 - 3:15 PM Coffee Break
* 3:15 - 5:00 PM Formulation of action plan and assignment of tasks

 

Return to [[Projects/Diffusion/2007_Project_Week_Contrasting_Tractography_Measures | Contrasting Tractography Project Page]]

SanteFe.Tractography.Conference

2007-09-28T18:46:48Z

Sgouttard:

= Goals =
We in NA-MIC, and our collaborating colleagues from BIRN, NAC and UIowa, are in a unique position to make a substanital contribution to the field of knowledge concerning the validation of medical image processing of Diffusion Tensor Image data. Among our faculty are leaders in the field of not only DTI analysis algorithm development, but also of validation and calibration. We seek to use our unique opportunity for multi-site collaboration to advance knowledge in this area for the benefit of clinical and computational scientists.

* To compare and contrast the results of tractography algorithms included in or supported by the NA-MIC Toolkit on a benchmark dataset of Diffusion Tensor Imaging (DTI) data. 
* To develop a framework for systematically and statistically comparing and contrasting these outcome measures mapped to specific manuscript preparation. 
* To map out appropriate leadership for each of the proposed manuscripts. 
* To initiate development of tutorials for tractography algorithms not yet in the NAMIC Training Compendium. 
* To propose methods for NA-MIC benchmarks of calibration and validation of tractography algorithms for further discussion at the 2008 AHM. 

== Conference Logistics ==

* October 1-2, 2007, 8:00 AM- 6:00 PM 
* The workshop is being held in the Governors Room at the Inn of the Governors, 101 W. Alameda, Sante Fe, NM 87501, 1-800-234-4534, http://www.innofthegovernors.com/ 
* We have booked a block of rooms for $169.00/night for single or double occupancy September 30- October 3, 2007 (Sunday through Tuesday nights). Our reservation code is "NAMIC" and the deadline for reservations is August 31, 2007. The price includes a full breakfast buffet, wireless internet access in the lobby, meeting room and sleeping rooms at no additional cost. 
* Fly into Albuquerque, NM. Information about shuttles from the airport to the hotel can be found here http://www.sandiashuttle.com/.

Many grateful thanks to John Rasure and Debbie Lynch of the MIND Institute for their assistance in making these arrangements.

==Registration==
* '''To register, add your name to the list of attendees below and make your flight and hotel reservations'''

* Questions about logistics and the content of the Conference should be addressed to Randy Gollub (rgollub at partners.org).

* '''This Conference is supported by the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on the National Centers for Biomedical Computing can be obtained from http://nihroadmap.nih.gov/bioinformatics'''.

== Conference Attendees ==

# Ross Whitaker, PhD
# Guido Gerig, PhD, Utah
# Casey Goodlett, Utah
# Carl-Fredrik Westin, PhD
# Marek Kubicki, MD, PhD
# Sylvain Bouix, PNL
# [[User:Randy|Randy Gollub, MD, PhD]], Harvard Medical School (Department of Psychiatry and Martinos Center, Department of Radiology, Massachussets General Hospital)
# [[User:SPujol|Sonia Pujol, PhD]], Harvard Medical School (Surgical Planning Laboratory, Department of Radiology, Brigham and Women's Hospital)
# H. Jeremy Bockholt, The MIND Institute
# [[User:Melonakos|John Melonakos]], Georgia Tech
# [[User:Kikinis|Ron Kikinis, MD]], SPL
# Tom Fletcher, Utah
# Anastasia Yendiki, MGH
# Allen Song, PhD Duke
# Tri Ngo, BWH
# Marc Niethammer, BWH
# Lauren O'Donnell, BWH
# Vincent Magnotta, Iowa
# [[ [Image:SantaFeTractography_Gouttard.ppt]‎ | Sylvain Gouttard, Utah]]
 

== Preparation for Workshop -- ''Important Information for all attendees'' ==

Suggestions: [[July31T-con |Notes from July 31 Planning T-con with detailed "To Dos"]]

Suggested background reading for workshop: 

#[[Media:AHM2006-validation-DTI-gg.ppt| Guido's 2006 AHM presentation on Validation strategies for DTI analysis]]
#[[Media:DWI.reproducibility.pdf]]
#[[http://cds.ismrm.org/protected/DiffusionWorkshop05 If any of you attended the 2005 ISMRM Workshop on Methods for Quantitative Diffusion of MRI of Human Brain and can get us access to the detailed summary, I have seen it and it might be very useful]]
#Presentations by and Fitzpatrick from the [http://idm.univ-rennes1.fr/VMIP/miccai2003/presentations.html MICCAI 2003 Tutorial on Validation in Medical Image Processing]
#Peruse the webpages associated with the [http://www.vuse.vanderbilt.edu/~image/registration/ Retrospective Image Registration Evaluation project]
#[http://ieeexplore.ieee.org/Xplore/login.jsp?url=/iel5/10818/34114/01624925.pdf anyone have access to this?]
#[[Media:BrainTissueClassifiers_BouixNeuroimage2007.pdf| Sylvain's segmentation comparison manuscript]]
#[[Media:MonkeyDTIStudy_Neuroimage2007.pdf| CF Westin's experimental study manuscript]]

Please complete the following items prior to the workshop.
'''This is hands-on Conference. All participants must come with their own computer loaded with the calibration data and the results of their own algorithm analysis. ''' 

'''Benchmark Datasets'''

== Agenda ==

== Welcome to Santa Fe Dinner ==

Sunday September 30th, 7:45 PM
La Casa Sena, 125 E. Palace, 505-988-9232 (www.lacasasena.com)

=== '''October 1, Meeting 8:30 AM - 6 PM''' ===
* 7:30- 8:30 AM Enjoy the breakfast buffet at the hotel
* 8:30 - 8:40 AM '''Goals of Conference''' Randy Gollub
* 8:40 - 11:45 AM '''Presentations of results from each of the participants & discussion:''' Guidelines: Please use this [[Media:NAMIC_Tractography_Conference_template.ppt| presentation template]].‎
Report-style, no details of methods known from previous Core-1 meetings, report about processing steps, parameters, user-interaction, user time, structure of results. Summary of difficulties and obstacles
**8:40 Guido Gerig set stage for series of presentations focusing on [http://www.na-mic.org/Wiki/index.php/Projects/Diffusion/Contrasting_Tractography_Measures tractography methods] and results
**8:50 Marek Kubicki Clinical Description of Fiber Bundles and Regions of Interest
**Session 1: 9:10-10:30
***9:10 Sonia Pujol (BWH) Streamline Tractography in Slicer using ROI and Whole Brain Seeding
***9:40 Sylvain Gouttard (Utah) FiberViewer
***10:05 Tri Ngo (BWH) Stochastic Tractography
** 10:30 -10:45 Coffee Break (place lunch order)
**Session 2: 10:45-12:30
***10:45 John Melonakos (GA) Geodesic Active Contours
***11:10 Ross Whitaker/Tom Fletcher (Utah) Volumetric Connectivity
***11:35 Casey Goodlett (Utah) DTI Atlas
*12:00 Lunch
*1:00 Ross Whitaker to kick-off discussion with summarizing ideas & focus
* 1:15 - 2:15 PM '''What did we learn?'''
** Problems with data quality (noise, on-scanner up-interpolation, size of datasets, Eddy current distortion, EPI distortion, artifacts etc.
** Problems with ROI definitions, appropriateness of methods given the data.
** Data issues: NRRD header interpretation, output formats, optimal calculation of tensors, others.
* 2:15 - 6:00 PM '''Where are we going with DTI processing?'''
** Towards statistical analysis of resulting measures obtained from processing: Approaches, pitfalls (like trying to count streamlines), statistics of tensors, statistics of FA values, functional analysis, multiple comparison correction, others.
** Discuss methods and metrics for contrasting/comparing outcomes of DTI analyses.
** Set detailed agenda for Tuesday
(coffee break somewhere above)

* 7:00 PM Dinner at local restaurant(s) to be found by wandering around town

=== '''October 2, 8:30 AM - 5 PM''' ===
* 7:30- 8:30 AM Enjoy the breakfast buffet at the hotel
* 8:30 - 8:50 AM Neurosurgical applications of tractography: Lauren O'Donnell (BHW)
* 8:50 - 9:00 AM Pilot results from the MIND multi-site DTI reliability dataset: Jeremy Bockholt (UNM)
* 9:00 - 10:15 '''Discuss what to do next on this project'''
* 10:15 -10:30 Coffee Break
* 10:30 - 11:45 '''Continue to formulate a plan for next steps on this project'''
* 11:45 - 1:00 PM Lunch together at local restaurant
* 1:00 - 3:00 PM '''?'''
* 3:00 - 3:15 PM Coffee Break
* 3:15 - 5:00 PM Formulation of action plan and assignment of tasks

 

Return to [[Projects/Diffusion/2007_Project_Week_Contrasting_Tractography_Measures | Contrasting Tractography Project Page]]

SanteFe.Tractography.Conference

2007-09-28T18:46:25Z

Sgouttard:

= Goals =
We in NA-MIC, and our collaborating colleagues from BIRN, NAC and UIowa, are in a unique position to make a substanital contribution to the field of knowledge concerning the validation of medical image processing of Diffusion Tensor Image data. Among our faculty are leaders in the field of not only DTI analysis algorithm development, but also of validation and calibration. We seek to use our unique opportunity for multi-site collaboration to advance knowledge in this area for the benefit of clinical and computational scientists.

* To compare and contrast the results of tractography algorithms included in or supported by the NA-MIC Toolkit on a benchmark dataset of Diffusion Tensor Imaging (DTI) data. 
* To develop a framework for systematically and statistically comparing and contrasting these outcome measures mapped to specific manuscript preparation. 
* To map out appropriate leadership for each of the proposed manuscripts. 
* To initiate development of tutorials for tractography algorithms not yet in the NAMIC Training Compendium. 
* To propose methods for NA-MIC benchmarks of calibration and validation of tractography algorithms for further discussion at the 2008 AHM. 

== Conference Logistics ==

* October 1-2, 2007, 8:00 AM- 6:00 PM 
* The workshop is being held in the Governors Room at the Inn of the Governors, 101 W. Alameda, Sante Fe, NM 87501, 1-800-234-4534, http://www.innofthegovernors.com/ 
* We have booked a block of rooms for $169.00/night for single or double occupancy September 30- October 3, 2007 (Sunday through Tuesday nights). Our reservation code is "NAMIC" and the deadline for reservations is August 31, 2007. The price includes a full breakfast buffet, wireless internet access in the lobby, meeting room and sleeping rooms at no additional cost. 
* Fly into Albuquerque, NM. Information about shuttles from the airport to the hotel can be found here http://www.sandiashuttle.com/.

Many grateful thanks to John Rasure and Debbie Lynch of the MIND Institute for their assistance in making these arrangements.

==Registration==
* '''To register, add your name to the list of attendees below and make your flight and hotel reservations'''

* Questions about logistics and the content of the Conference should be addressed to Randy Gollub (rgollub at partners.org).

* '''This Conference is supported by the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on the National Centers for Biomedical Computing can be obtained from http://nihroadmap.nih.gov/bioinformatics'''.

== Conference Attendees ==

# Ross Whitaker, PhD
# Guido Gerig, PhD, Utah
# Casey Goodlett, Utah
# Carl-Fredrik Westin, PhD
# Marek Kubicki, MD, PhD
# Sylvain Bouix, PNL
# [[User:Randy|Randy Gollub, MD, PhD]], Harvard Medical School (Department of Psychiatry and Martinos Center, Department of Radiology, Massachussets General Hospital)
# [[User:SPujol|Sonia Pujol, PhD]], Harvard Medical School (Surgical Planning Laboratory, Department of Radiology, Brigham and Women's Hospital)
# H. Jeremy Bockholt, The MIND Institute
# [[User:Melonakos|John Melonakos]], Georgia Tech
# [[User:Kikinis|Ron Kikinis, MD]], SPL
# Tom Fletcher, Utah
# Anastasia Yendiki, MGH
# Allen Song, PhD Duke
# Tri Ngo, BWH
# Marc Niethammer, BWH
# Lauren O'Donnell, BWH
# Vincent Magnotta, Iowa
# [[ Image:SantaFeTractography_Gouttard.ppt‎ | Sylvain Gouttard, Utah]]
 

== Preparation for Workshop -- ''Important Information for all attendees'' ==

Suggestions: [[July31T-con |Notes from July 31 Planning T-con with detailed "To Dos"]]

Suggested background reading for workshop: 

#[[Media:AHM2006-validation-DTI-gg.ppt| Guido's 2006 AHM presentation on Validation strategies for DTI analysis]]
#[[Media:DWI.reproducibility.pdf]]
#[[http://cds.ismrm.org/protected/DiffusionWorkshop05 If any of you attended the 2005 ISMRM Workshop on Methods for Quantitative Diffusion of MRI of Human Brain and can get us access to the detailed summary, I have seen it and it might be very useful]]
#Presentations by and Fitzpatrick from the [http://idm.univ-rennes1.fr/VMIP/miccai2003/presentations.html MICCAI 2003 Tutorial on Validation in Medical Image Processing]
#Peruse the webpages associated with the [http://www.vuse.vanderbilt.edu/~image/registration/ Retrospective Image Registration Evaluation project]
#[http://ieeexplore.ieee.org/Xplore/login.jsp?url=/iel5/10818/34114/01624925.pdf anyone have access to this?]
#[[Media:BrainTissueClassifiers_BouixNeuroimage2007.pdf| Sylvain's segmentation comparison manuscript]]
#[[Media:MonkeyDTIStudy_Neuroimage2007.pdf| CF Westin's experimental study manuscript]]

Please complete the following items prior to the workshop.
'''This is hands-on Conference. All participants must come with their own computer loaded with the calibration data and the results of their own algorithm analysis. ''' 

'''Benchmark Datasets'''

== Agenda ==

== Welcome to Santa Fe Dinner ==

Sunday September 30th, 7:45 PM
La Casa Sena, 125 E. Palace, 505-988-9232 (www.lacasasena.com)

=== '''October 1, Meeting 8:30 AM - 6 PM''' ===
* 7:30- 8:30 AM Enjoy the breakfast buffet at the hotel
* 8:30 - 8:40 AM '''Goals of Conference''' Randy Gollub
* 8:40 - 11:45 AM '''Presentations of results from each of the participants & discussion:''' Guidelines: Please use this [[Media:NAMIC_Tractography_Conference_template.ppt| presentation template]].‎
Report-style, no details of methods known from previous Core-1 meetings, report about processing steps, parameters, user-interaction, user time, structure of results. Summary of difficulties and obstacles
**8:40 Guido Gerig set stage for series of presentations focusing on [http://www.na-mic.org/Wiki/index.php/Projects/Diffusion/Contrasting_Tractography_Measures tractography methods] and results
**8:50 Marek Kubicki Clinical Description of Fiber Bundles and Regions of Interest
**Session 1: 9:10-10:30
***9:10 Sonia Pujol (BWH) Streamline Tractography in Slicer using ROI and Whole Brain Seeding
***9:40 Sylvain Gouttard (Utah) FiberViewer
***10:05 Tri Ngo (BWH) Stochastic Tractography
** 10:30 -10:45 Coffee Break (place lunch order)
**Session 2: 10:45-12:30
***10:45 John Melonakos (GA) Geodesic Active Contours
***11:10 Ross Whitaker/Tom Fletcher (Utah) Volumetric Connectivity
***11:35 Casey Goodlett (Utah) DTI Atlas
*12:00 Lunch
*1:00 Ross Whitaker to kick-off discussion with summarizing ideas & focus
* 1:15 - 2:15 PM '''What did we learn?'''
** Problems with data quality (noise, on-scanner up-interpolation, size of datasets, Eddy current distortion, EPI distortion, artifacts etc.
** Problems with ROI definitions, appropriateness of methods given the data.
** Data issues: NRRD header interpretation, output formats, optimal calculation of tensors, others.
* 2:15 - 6:00 PM '''Where are we going with DTI processing?'''
** Towards statistical analysis of resulting measures obtained from processing: Approaches, pitfalls (like trying to count streamlines), statistics of tensors, statistics of FA values, functional analysis, multiple comparison correction, others.
** Discuss methods and metrics for contrasting/comparing outcomes of DTI analyses.
** Set detailed agenda for Tuesday
(coffee break somewhere above)

* 7:00 PM Dinner at local restaurant(s) to be found by wandering around town

=== '''October 2, 8:30 AM - 5 PM''' ===
* 7:30- 8:30 AM Enjoy the breakfast buffet at the hotel
* 8:30 - 8:50 AM Neurosurgical applications of tractography: Lauren O'Donnell (BHW)
* 8:50 - 9:00 AM Pilot results from the MIND multi-site DTI reliability dataset: Jeremy Bockholt (UNM)
* 9:00 - 10:15 '''Discuss what to do next on this project'''
* 10:15 -10:30 Coffee Break
* 10:30 - 11:45 '''Continue to formulate a plan for next steps on this project'''
* 11:45 - 1:00 PM Lunch together at local restaurant
* 1:00 - 3:00 PM '''?'''
* 3:00 - 3:15 PM Coffee Break
* 3:15 - 5:00 PM Formulation of action plan and assignment of tasks

 

Return to [[Projects/Diffusion/2007_Project_Week_Contrasting_Tractography_Measures | Contrasting Tractography Project Page]]

SanteFe.Tractography.Conference

2007-09-28T18:44:27Z

Sgouttard:

= Goals =
We in NA-MIC, and our collaborating colleagues from BIRN, NAC and UIowa, are in a unique position to make a substanital contribution to the field of knowledge concerning the validation of medical image processing of Diffusion Tensor Image data. Among our faculty are leaders in the field of not only DTI analysis algorithm development, but also of validation and calibration. We seek to use our unique opportunity for multi-site collaboration to advance knowledge in this area for the benefit of clinical and computational scientists.

* To compare and contrast the results of tractography algorithms included in or supported by the NA-MIC Toolkit on a benchmark dataset of Diffusion Tensor Imaging (DTI) data. 
* To develop a framework for systematically and statistically comparing and contrasting these outcome measures mapped to specific manuscript preparation. 
* To map out appropriate leadership for each of the proposed manuscripts. 
* To initiate development of tutorials for tractography algorithms not yet in the NAMIC Training Compendium. 
* To propose methods for NA-MIC benchmarks of calibration and validation of tractography algorithms for further discussion at the 2008 AHM. 

== Conference Logistics ==

* October 1-2, 2007, 8:00 AM- 6:00 PM 
* The workshop is being held in the Governors Room at the Inn of the Governors, 101 W. Alameda, Sante Fe, NM 87501, 1-800-234-4534, http://www.innofthegovernors.com/ 
* We have booked a block of rooms for $169.00/night for single or double occupancy September 30- October 3, 2007 (Sunday through Tuesday nights). Our reservation code is "NAMIC" and the deadline for reservations is August 31, 2007. The price includes a full breakfast buffet, wireless internet access in the lobby, meeting room and sleeping rooms at no additional cost. 
* Fly into Albuquerque, NM. Information about shuttles from the airport to the hotel can be found here http://www.sandiashuttle.com/.

Many grateful thanks to John Rasure and Debbie Lynch of the MIND Institute for their assistance in making these arrangements.

==Registration==
* '''To register, add your name to the list of attendees below and make your flight and hotel reservations'''

* Questions about logistics and the content of the Conference should be addressed to Randy Gollub (rgollub at partners.org).

* '''This Conference is supported by the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on the National Centers for Biomedical Computing can be obtained from http://nihroadmap.nih.gov/bioinformatics'''.

== Conference Attendees ==

# Ross Whitaker, PhD
# Guido Gerig, PhD, Utah
# Casey Goodlett, Utah
# Carl-Fredrik Westin, PhD
# Marek Kubicki, MD, PhD
# Sylvain Bouix, PNL
# [[User:Randy|Randy Gollub, MD, PhD]], Harvard Medical School (Department of Psychiatry and Martinos Center, Department of Radiology, Massachussets General Hospital)
# [[User:SPujol|Sonia Pujol, PhD]], Harvard Medical School (Surgical Planning Laboratory, Department of Radiology, Brigham and Women's Hospital)
# H. Jeremy Bockholt, The MIND Institute
# [[User:Melonakos|John Melonakos]], Georgia Tech
# [[User:Kikinis|Ron Kikinis, MD]], SPL
# Tom Fletcher, Utah
# Anastasia Yendiki, MGH
# Allen Song, PhD Duke
# Tri Ngo, BWH
# Marc Niethammer, BWH
# Lauren O'Donnell, BWH
# Vincent Magnotta, Iowa
# [[ SantaFeTractography_Gouttard.ppt‎ | Sylvain Gouttard, Utah]]
 

== Preparation for Workshop -- ''Important Information for all attendees'' ==

Suggestions: [[July31T-con |Notes from July 31 Planning T-con with detailed "To Dos"]]

Suggested background reading for workshop: 

#[[Media:AHM2006-validation-DTI-gg.ppt| Guido's 2006 AHM presentation on Validation strategies for DTI analysis]]
#[[Media:DWI.reproducibility.pdf]]
#[[http://cds.ismrm.org/protected/DiffusionWorkshop05 If any of you attended the 2005 ISMRM Workshop on Methods for Quantitative Diffusion of MRI of Human Brain and can get us access to the detailed summary, I have seen it and it might be very useful]]
#Presentations by and Fitzpatrick from the [http://idm.univ-rennes1.fr/VMIP/miccai2003/presentations.html MICCAI 2003 Tutorial on Validation in Medical Image Processing]
#Peruse the webpages associated with the [http://www.vuse.vanderbilt.edu/~image/registration/ Retrospective Image Registration Evaluation project]
#[http://ieeexplore.ieee.org/Xplore/login.jsp?url=/iel5/10818/34114/01624925.pdf anyone have access to this?]
#[[Media:BrainTissueClassifiers_BouixNeuroimage2007.pdf| Sylvain's segmentation comparison manuscript]]
#[[Media:MonkeyDTIStudy_Neuroimage2007.pdf| CF Westin's experimental study manuscript]]

Please complete the following items prior to the workshop.
'''This is hands-on Conference. All participants must come with their own computer loaded with the calibration data and the results of their own algorithm analysis. ''' 

'''Benchmark Datasets'''

== Agenda ==

== Welcome to Santa Fe Dinner ==

Sunday September 30th, 7:45 PM
La Casa Sena, 125 E. Palace, 505-988-9232 (www.lacasasena.com)

=== '''October 1, Meeting 8:30 AM - 6 PM''' ===
* 7:30- 8:30 AM Enjoy the breakfast buffet at the hotel
* 8:30 - 8:40 AM '''Goals of Conference''' Randy Gollub
* 8:40 - 11:45 AM '''Presentations of results from each of the participants & discussion:''' Guidelines: Please use this [[Media:NAMIC_Tractography_Conference_template.ppt| presentation template]].‎
Report-style, no details of methods known from previous Core-1 meetings, report about processing steps, parameters, user-interaction, user time, structure of results. Summary of difficulties and obstacles
**8:40 Guido Gerig set stage for series of presentations focusing on [http://www.na-mic.org/Wiki/index.php/Projects/Diffusion/Contrasting_Tractography_Measures tractography methods] and results
**8:50 Marek Kubicki Clinical Description of Fiber Bundles and Regions of Interest
**Session 1: 9:10-10:30
***9:10 Sonia Pujol (BWH) Streamline Tractography in Slicer using ROI and Whole Brain Seeding
***9:40 Sylvain Gouttard (Utah) FiberViewer
***10:05 Tri Ngo (BWH) Stochastic Tractography
** 10:30 -10:45 Coffee Break (place lunch order)
**Session 2: 10:45-12:30
***10:45 John Melonakos (GA) Geodesic Active Contours
***11:10 Ross Whitaker/Tom Fletcher (Utah) Volumetric Connectivity
***11:35 Casey Goodlett (Utah) DTI Atlas
*12:00 Lunch
*1:00 Ross Whitaker to kick-off discussion with summarizing ideas & focus
* 1:15 - 2:15 PM '''What did we learn?'''
** Problems with data quality (noise, on-scanner up-interpolation, size of datasets, Eddy current distortion, EPI distortion, artifacts etc.
** Problems with ROI definitions, appropriateness of methods given the data.
** Data issues: NRRD header interpretation, output formats, optimal calculation of tensors, others.
* 2:15 - 6:00 PM '''Where are we going with DTI processing?'''
** Towards statistical analysis of resulting measures obtained from processing: Approaches, pitfalls (like trying to count streamlines), statistics of tensors, statistics of FA values, functional analysis, multiple comparison correction, others.
** Discuss methods and metrics for contrasting/comparing outcomes of DTI analyses.
** Set detailed agenda for Tuesday
(coffee break somewhere above)

* 7:00 PM Dinner at local restaurant(s) to be found by wandering around town

=== '''October 2, 8:30 AM - 5 PM''' ===
* 7:30- 8:30 AM Enjoy the breakfast buffet at the hotel
* 8:30 - 8:50 AM Neurosurgical applications of tractography: Lauren O'Donnell (BHW)
* 8:50 - 9:00 AM Pilot results from the MIND multi-site DTI reliability dataset: Jeremy Bockholt (UNM)
* 9:00 - 10:15 '''Discuss what to do next on this project'''
* 10:15 -10:30 Coffee Break
* 10:30 - 11:45 '''Continue to formulate a plan for next steps on this project'''
* 11:45 - 1:00 PM Lunch together at local restaurant
* 1:00 - 3:00 PM '''?'''
* 3:00 - 3:15 PM Coffee Break
* 3:15 - 5:00 PM Formulation of action plan and assignment of tasks

 

Return to [[Projects/Diffusion/2007_Project_Week_Contrasting_Tractography_Measures | Contrasting Tractography Project Page]]

SanteFe.Tractography.Conference

2007-09-28T18:44:01Z

Sgouttard:

= Goals =
We in NA-MIC, and our collaborating colleagues from BIRN, NAC and UIowa, are in a unique position to make a substanital contribution to the field of knowledge concerning the validation of medical image processing of Diffusion Tensor Image data. Among our faculty are leaders in the field of not only DTI analysis algorithm development, but also of validation and calibration. We seek to use our unique opportunity for multi-site collaboration to advance knowledge in this area for the benefit of clinical and computational scientists.

* To compare and contrast the results of tractography algorithms included in or supported by the NA-MIC Toolkit on a benchmark dataset of Diffusion Tensor Imaging (DTI) data. 
* To develop a framework for systematically and statistically comparing and contrasting these outcome measures mapped to specific manuscript preparation. 
* To map out appropriate leadership for each of the proposed manuscripts. 
* To initiate development of tutorials for tractography algorithms not yet in the NAMIC Training Compendium. 
* To propose methods for NA-MIC benchmarks of calibration and validation of tractography algorithms for further discussion at the 2008 AHM. 

== Conference Logistics ==

* October 1-2, 2007, 8:00 AM- 6:00 PM 
* The workshop is being held in the Governors Room at the Inn of the Governors, 101 W. Alameda, Sante Fe, NM 87501, 1-800-234-4534, http://www.innofthegovernors.com/ 
* We have booked a block of rooms for $169.00/night for single or double occupancy September 30- October 3, 2007 (Sunday through Tuesday nights). Our reservation code is "NAMIC" and the deadline for reservations is August 31, 2007. The price includes a full breakfast buffet, wireless internet access in the lobby, meeting room and sleeping rooms at no additional cost. 
* Fly into Albuquerque, NM. Information about shuttles from the airport to the hotel can be found here http://www.sandiashuttle.com/.

Many grateful thanks to John Rasure and Debbie Lynch of the MIND Institute for their assistance in making these arrangements.

==Registration==
* '''To register, add your name to the list of attendees below and make your flight and hotel reservations'''

* Questions about logistics and the content of the Conference should be addressed to Randy Gollub (rgollub at partners.org).

* '''This Conference is supported by the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on the National Centers for Biomedical Computing can be obtained from http://nihroadmap.nih.gov/bioinformatics'''.

== Conference Attendees ==

# Ross Whitaker, PhD
# Guido Gerig, PhD, Utah
# Casey Goodlett, Utah
# Carl-Fredrik Westin, PhD
# Marek Kubicki, MD, PhD
# Sylvain Bouix, PNL
# [[User:Randy|Randy Gollub, MD, PhD]], Harvard Medical School (Department of Psychiatry and Martinos Center, Department of Radiology, Massachussets General Hospital)
# [[User:SPujol|Sonia Pujol, PhD]], Harvard Medical School (Surgical Planning Laboratory, Department of Radiology, Brigham and Women's Hospital)
# H. Jeremy Bockholt, The MIND Institute
# [[User:Melonakos|John Melonakos]], Georgia Tech
# [[User:Kikinis|Ron Kikinis, MD]], SPL
# Tom Fletcher, Utah
# Anastasia Yendiki, MGH
# Allen Song, PhD Duke
# Tri Ngo, BWH
# Marc Niethammer, BWH
# Lauren O'Donnell, BWH
# Vincent Magnotta, Iowa
# [[Sylvain Gouttard, Utah | SantaFeTractography_Gouttard.ppt‎ ]]
 

== Preparation for Workshop -- ''Important Information for all attendees'' ==

Suggestions: [[July31T-con |Notes from July 31 Planning T-con with detailed "To Dos"]]

Suggested background reading for workshop: 

#[[Media:AHM2006-validation-DTI-gg.ppt| Guido's 2006 AHM presentation on Validation strategies for DTI analysis]]
#[[Media:DWI.reproducibility.pdf]]
#[[http://cds.ismrm.org/protected/DiffusionWorkshop05 If any of you attended the 2005 ISMRM Workshop on Methods for Quantitative Diffusion of MRI of Human Brain and can get us access to the detailed summary, I have seen it and it might be very useful]]
#Presentations by and Fitzpatrick from the [http://idm.univ-rennes1.fr/VMIP/miccai2003/presentations.html MICCAI 2003 Tutorial on Validation in Medical Image Processing]
#Peruse the webpages associated with the [http://www.vuse.vanderbilt.edu/~image/registration/ Retrospective Image Registration Evaluation project]
#[http://ieeexplore.ieee.org/Xplore/login.jsp?url=/iel5/10818/34114/01624925.pdf anyone have access to this?]
#[[Media:BrainTissueClassifiers_BouixNeuroimage2007.pdf| Sylvain's segmentation comparison manuscript]]
#[[Media:MonkeyDTIStudy_Neuroimage2007.pdf| CF Westin's experimental study manuscript]]

Please complete the following items prior to the workshop.
'''This is hands-on Conference. All participants must come with their own computer loaded with the calibration data and the results of their own algorithm analysis. ''' 

'''Benchmark Datasets'''

== Agenda ==

== Welcome to Santa Fe Dinner ==

Sunday September 30th, 7:45 PM
La Casa Sena, 125 E. Palace, 505-988-9232 (www.lacasasena.com)

=== '''October 1, Meeting 8:30 AM - 6 PM''' ===
* 7:30- 8:30 AM Enjoy the breakfast buffet at the hotel
* 8:30 - 8:40 AM '''Goals of Conference''' Randy Gollub
* 8:40 - 11:45 AM '''Presentations of results from each of the participants & discussion:''' Guidelines: Please use this [[Media:NAMIC_Tractography_Conference_template.ppt| presentation template]].‎
Report-style, no details of methods known from previous Core-1 meetings, report about processing steps, parameters, user-interaction, user time, structure of results. Summary of difficulties and obstacles
**8:40 Guido Gerig set stage for series of presentations focusing on [http://www.na-mic.org/Wiki/index.php/Projects/Diffusion/Contrasting_Tractography_Measures tractography methods] and results
**8:50 Marek Kubicki Clinical Description of Fiber Bundles and Regions of Interest
**Session 1: 9:10-10:30
***9:10 Sonia Pujol (BWH) Streamline Tractography in Slicer using ROI and Whole Brain Seeding
***9:40 Sylvain Gouttard (Utah) FiberViewer
***10:05 Tri Ngo (BWH) Stochastic Tractography
** 10:30 -10:45 Coffee Break (place lunch order)
**Session 2: 10:45-12:30
***10:45 John Melonakos (GA) Geodesic Active Contours
***11:10 Ross Whitaker/Tom Fletcher (Utah) Volumetric Connectivity
***11:35 Casey Goodlett (Utah) DTI Atlas
*12:00 Lunch
*1:00 Ross Whitaker to kick-off discussion with summarizing ideas & focus
* 1:15 - 2:15 PM '''What did we learn?'''
** Problems with data quality (noise, on-scanner up-interpolation, size of datasets, Eddy current distortion, EPI distortion, artifacts etc.
** Problems with ROI definitions, appropriateness of methods given the data.
** Data issues: NRRD header interpretation, output formats, optimal calculation of tensors, others.
* 2:15 - 6:00 PM '''Where are we going with DTI processing?'''
** Towards statistical analysis of resulting measures obtained from processing: Approaches, pitfalls (like trying to count streamlines), statistics of tensors, statistics of FA values, functional analysis, multiple comparison correction, others.
** Discuss methods and metrics for contrasting/comparing outcomes of DTI analyses.
** Set detailed agenda for Tuesday
(coffee break somewhere above)

* 7:00 PM Dinner at local restaurant(s) to be found by wandering around town

=== '''October 2, 8:30 AM - 5 PM''' ===
* 7:30- 8:30 AM Enjoy the breakfast buffet at the hotel
* 8:30 - 8:50 AM Neurosurgical applications of tractography: Lauren O'Donnell (BHW)
* 8:50 - 9:00 AM Pilot results from the MIND multi-site DTI reliability dataset: Jeremy Bockholt (UNM)
* 9:00 - 10:15 '''Discuss what to do next on this project'''
* 10:15 -10:30 Coffee Break
* 10:30 - 11:45 '''Continue to formulate a plan for next steps on this project'''
* 11:45 - 1:00 PM Lunch together at local restaurant
* 1:00 - 3:00 PM '''?'''
* 3:00 - 3:15 PM Coffee Break
* 3:15 - 5:00 PM Formulation of action plan and assignment of tasks

 

Return to [[Projects/Diffusion/2007_Project_Week_Contrasting_Tractography_Measures | Contrasting Tractography Project Page]]

File:SantaFeTractography Gouttard.ppt

2007-09-28T18:43:12Z

Sgouttard: Presentation from Sylvain GOUTTARD of Utah/UNC results for the SantaFe meeting

Presentation from Sylvain GOUTTARD of Utah/UNC results for the SantaFe meeting

Slicer3:Module Documentation

2007-09-19T16:19:04Z

Sgouttard:

Please do not edit these pages until the template has been finalized!

==Slicer3 Base Modules==

* [[Slicer3:Module:Cameras | Cameras ]]
* [[Slicer3:Module:Color | Color ]]
* [[Slicer3:Module:Data | Data ]]
* [[Slicer3:Module:EMSegment | EMSegment ]]
* [[Slicer3:Module:Editor | Editor ]]
* [[Slicer3:Module:Fiducials | Fiducials ]]
* [[Slicer3:Module:GradientAnisotropicDiffusionFilter | Gradient Anisotropic Diffusion Filter ]]
* [[Slicer3:Module:Models | Models ]]
* [[Slicer3:Module:NeuroNav | NeuroNav ]]
* [[Slicer3:Module:QueryAtlas | Query Atlas ]]
* [[Slicer3:Module:Slices | Slices ]]
* [[Slicer3:Module:Transforms | Transforms ]]
* [[Slicer3:Module:Volumes | Volumes ]]

==Converter Modules==
* [[Slicer3:Module:Create_a_DICOM_Series | Create a DICOM Series ]]
* [[Slicer3:Module:GE_Dicom_to_NRRD_Converter | GE DICOM to NRRD Converter ]]

==Demonstration Modules==
* [[Slicer3:Module:Execution_Model_Tour | Execution Model Tour ]]

==Diffusion Tensor Modules==

===Estimation===
* [[Slicer3:Module:Diffusion_Tensor_Estimation | Diffusion Tensor Estimation ]]

===Test===
* [[Slicer3:Module:Simple_IO_Test | Simple IO Test ]]

==Diffusion Weighted Imaging Modules==

===Test===
* [[Slicer3:Module:Simple_DWI_IO_Test | Simple DWI IO Test ]]

==Filtering Modules==
* [[Slicer3:Module:Checkerboard_Filter | Checkerboard Filter ]]
* [[Slicer3:Module:Histogram_Matching | Histogram Matching ]]
* [[Slicer3:Module:Otsu_Threshold | Otsu Threshold ]]
* [[Slicer3:Module:Resample_Volume | Resample Volume ]]
* [[Slicer3:Module:Voting_Binary_Hole_Filling | Voting Binary Hole Filling ]]
* [[Slicer3:Module:Rician_Noise_Removal | Rician noise removal in tensor images]]

===Arithmetic===
* [[Slicer3:Module:Add_Images | Add Images ]]
* [[Slicer3:Module:Subtract_Images | Subtract Images ]]

===DWI===
*[[Slicer3:Module:Rician_Noise_Removal | Rician noise removal in DWI]]

===Denoising===
* [[Slicer3:Module:Curvature_Anisotropic_Diffusion | Curvature Anisotropic Diffusion ]]
* [[Slicer3:Module:Gradient_Anisotropic_Diffusion | Gradient Anisotropic Diffusion ]]
* [[Slicer3:Module:Median_Filter | Median Filter ]]

===Morphology===
* [[Slicer3:Module:Grayscale_Fill_Hole | Grayscale Fill Hole ]]
* [[Slicer3:Module:Grayscale_Grind_Peak | Grayscale Grind Peak]]

==Model Generation Modules==
* [[Slicer3:Module:Grayscale_Model_Maker | Grayscale Model Maker ]]
* [[Slicer3:Module:Model_Maker | Model Maker ]]

==Registration Modules==
* [[Slicer3:Module:Affine_registration | Affine Registration ]]
* [[Slicer3:Module:Deformable_BSpline_registration | Deformable BSpline Registration ]]
* [[Slicer3:Module:Linear_registration | Linear Registration]]

==Segmentation Modules==
* [[Slicer3:Module:Otsu_Threshold_Segmentation | Otsu Threshold Segmentation ]]
* [[Slicer3:Module:Simple_region_growing | Simple Region Growing ]]

==Tractography Modules==
* [[Slicer3:Module:Tractography | Tractography ]]

Slicer3:Module:Rician Noise Removal

2007-09-19T16:17:00Z

Sgouttard:

===Module Name===
Rician Noise Removal in Diffusion Tensor MRI (DWI and tensors)

{|
|[[Image:RicianTensorCorrectionImage.png|thumb|280px|Caption 1]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Filtering DWI and tensors

===Authors, Collaborators & Contact===
* Saurav Basu: University of Utah
* Thomas Fletcher, University of Utah
* Ross Withaker, University of Utah
* Contact: Thomas Fletcher

===Module Description===
Rician noise introduces a bias into MRI measurements that
can have a signiﬁcant impact on the shapes and orientations of ten-
sors in diﬀusion tensor magnetic resonance images. This is less of a
problem in structural MRI, because this bias is signal dependent and
it does not seriously impair tissue identiﬁcation or clinical diagnoses.
However, diﬀusion imaging is used extensively for quantitative evalua-
tions, and the tensors used in those evaluations are biased in ways that
depend on orientation and signal levels. This paper presents a strat-
egy for ﬁltering diﬀusion tensor magnetic resonance images that ad-
dresses these issues. The method is a maximum a posteriori estima-
tion technique that operates directly on the diﬀusion weighted images
and accounts for the biases introduced by Rician noise. We account for
Rician noise through a data likelihood term that is combined with a
spatial smoothing prior. The method compares favorably with several
other approaches from the literature, including methods that ﬁlter dif-
fusion weighted imagery and those that operate directly on the diﬀusion
tensors.

== Usage ==

===DWI filtering===

====Examples, Use Cases & Tutorials====

USAGE
--------------
dwiFilter <arguments>
Arguments:
1. Input File Name
2. Output File Name
3. NumIterations
4. Conductance
5. TimeStep
6. Filter Type : (Simple Aniso-0,Chi Squared-1,Rician-2,Gaussian-3)
7. Sigma for bias correction
8. Lamda (Rician Correction Term)
9. Lamda (Gaussian Correction Term)

Argument Description:

<Input File Name>
Name of the DWI file to be filtered. For example
<noisyDWI_10.nhdr> is a noisy DWI file provided
in the data directory. It was generated by adding
synthetic Rician noise with a sigma=10 to a cleanDWI.nhdr

<Output File Name>
Name of the filtered DWI file. For example
<filteredDWI.nhdr>

<NumIterations>
Number of iterations you want to run the filter for.

<Conductance>
The value of the conductance term in anisotropic
diffusion filtering (Ex: 1.0)
Note: Large Conductance will oversmooth the image
It is important to tune the conductance to obtain
best results.

<Time Step>
This determines the step size in the gradient
descent. It can be atmost 0.0625.

<Filter Type>
Can Take 3 values:
0 means perform simple anisotropic diffusion

* - 1 means perform Chi-Squared smoothing (square the image and perform anisotropic diffusion and then subtract the variance of the noise, and take square root. (The square of a Rice distribution is a Chi Squared distribution with known bias equal to the variance of the noise) (Refer:Max likelihood Est. of Rician Ditribution Parameters. Sijbers et. al)
* - 2 means Perform Rician bias correction filtering.(Refer: Rician Noise Removal in DT-MRI.)
* - 3 is same as 2 except use a Gaussian Attachment Term .

<Sigma>
Estimate of noise in the data.
This can be done by squaring the airvoxels
in the real data. The sum of square of all
the intensities in the air region should equal
2*variance of the noise in the data.
(Sijbers et. al)

<lamda1, lamda2>
The weights for the Rician and Gaussian
attachment terms.

EXAMPLE
-------------
dwiFilter ../data/noisyDWI_10.nhdr filteredDWI.nhdr 1 1.0 0.0625 2 10 100 0

Filters the noisyDWI_10.nhdr for 1 iteration with a conductance of 1.0
timeStep 0.0625 using Rician filtering with a Rician attachement term
weight of 100. The estimate of noise in the input image is a sigma of 10
The filtered image is filteredDWI.nhdr.

===Tensor filtering===

Usage
--------------
tensorDiffuse <Arguments>
1. FilterType:(0-Euclidean, 1-Log Space,2-Riemannian)
2. numIterations:Iterations For Anisotropic Diffusion
3. timeStep:timeStep Used in Anisotropic Diffusion
4. conductance:Conductance used for Anisotropic Diffusion
5. Input (filename of input data)
6. Output (filename of output data)

Arguments 2,3,4 have the same meaning as described for dwiFilter (see above).

Argument 1 describes the filter type
* - 0: Euclidean Space filtering (tensors are treated as 6-d vectors)
* - 1: Log Space filtering (Fast and Simple Calculus on Tensors in the Log-Euclidean Framework. In J. Duncan and G. Gerig, editors, Proceedings of the 8th Int. Conf. on Medical Image Computing and Computer-Assisted Intervention - MICCAI 2005, Part I, volume 3749 of LNCS, Palm Springs, CA, USA, October 26-29, pages 115-122, 2005. Springer Verlag)
* - 2. Riemannian Space Filtering(A Riemannian Framework for the Processing of Tensor-Valued Images. In Ole Fogh Olsen, Luc Florak, and Arjan Kuijper, editors, Deep Structure, Singularities, and Computer Vision (DSSCV), number 3753 of LNCS, pages 112-123, June 2005. Springer Verlag.)

Currently, the Riemannian filter adjustment for negative eigen-values
is hard-coded in the source file.

Argument 5 is the name of the noisyTensor input.
Argument 6 is the name of the output tensor file

EXAMPLE
--------------
tensorFilter 2 1 0.0625 1.0 noisyTensor_10.nhdr FilteredTensor.nhrd

===Quick Tour of Features and Use===
List all the panels in your interface, their features, what they mean, and how to use them. For instance:

* '''Input panel:'''
* '''Parameters panel:'''
* '''Output panel:'''
* '''Viewing panel:'''

== Development ==

===Known bugs===

Follow this link to the Slicer3 bug tracker:

http://na-mic.org/Mantis/main_page.php

===Usability issues===

Follow this link to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing:

http://na-mic.org/Mantis/main_page.php

===Source code & documentation===

Customize following links for your module:

http://www.na-mic.org/ViewVC/index.cgi/

Links to documentation generated by doxygen:

http://www.na-mic.org/Slicer/Documentation/Slicer3/html/

== More Information ==

===Acknowledgement===
This work is part of the National Alliance for Medical Image Computing
(NAMIC), funded by the National Institutes of Health through the NIH Roadmap
for Medical Research, Grant U54 EB005149. Information on the National Centers
for Biomedical Computing can be obtained from http://nihroadmap.nih.gov/
bioinformatics. Funding for this work has also been provided by Center for
Integrative Biomedical Computing, NIH NCRR Project 2-P41-RR12553-07. We
thank Weili Lin and Guido Gerig from the University of North Carolina for
providing us with the DW-MRI data. Glyph visualizations created with Teem
(http://teem.sf.net).

===References===
Basu, S., Fletcher, P.T., Whitaker, R.T. Rician Noise Removal in Diffusion Tensor MRI. In Medical Image Computing and Computer Assisted Intervention (MICCAI), LNCS 4190, pp. 117-125, October, 2006.
[[http://www.sci.utah.edu/~fletcher/BasuDTIFilteringMICCAI2006.pdf | Paper link ]]

Slicer3:Module:Rician Noise Removal

2007-09-19T16:16:41Z

Sgouttard:

===Module Name===
Rician Noise Removal in Diffusion Tensor MRI (DWI and tensors)

{|
|[[Image:RicianTensorCorrectionImage.png|thumb|280px|Caption 1]]
|[[Image:screenshotBlank.png|thumb|280px|Caption 2]]
|[[Image:screenshotBlank.png|thumb|280px|Caption 3]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Filtering DWI and tensors

===Authors, Collaborators & Contact===
* Saurav Basu: University of Utah
* Thomas Fletcher, University of Utah
* Ross Withaker, University of Utah
* Contact: Thomas Fletcher

===Module Description===
Rician noise introduces a bias into MRI measurements that
can have a signiﬁcant impact on the shapes and orientations of ten-
sors in diﬀusion tensor magnetic resonance images. This is less of a
problem in structural MRI, because this bias is signal dependent and
it does not seriously impair tissue identiﬁcation or clinical diagnoses.
However, diﬀusion imaging is used extensively for quantitative evalua-
tions, and the tensors used in those evaluations are biased in ways that
depend on orientation and signal levels. This paper presents a strat-
egy for ﬁltering diﬀusion tensor magnetic resonance images that ad-
dresses these issues. The method is a maximum a posteriori estima-
tion technique that operates directly on the diﬀusion weighted images
and accounts for the biases introduced by Rician noise. We account for
Rician noise through a data likelihood term that is combined with a
spatial smoothing prior. The method compares favorably with several
other approaches from the literature, including methods that ﬁlter dif-
fusion weighted imagery and those that operate directly on the diﬀusion
tensors.

== Usage ==

===DWI filtering===

====Examples, Use Cases & Tutorials====

USAGE
--------------
dwiFilter <arguments>
Arguments:
1. Input File Name
2. Output File Name
3. NumIterations
4. Conductance
5. TimeStep
6. Filter Type : (Simple Aniso-0,Chi Squared-1,Rician-2,Gaussian-3)
7. Sigma for bias correction
8. Lamda (Rician Correction Term)
9. Lamda (Gaussian Correction Term)

Argument Description:

<Input File Name>
Name of the DWI file to be filtered. For example
<noisyDWI_10.nhdr> is a noisy DWI file provided
in the data directory. It was generated by adding
synthetic Rician noise with a sigma=10 to a cleanDWI.nhdr

<Output File Name>
Name of the filtered DWI file. For example
<filteredDWI.nhdr>

<NumIterations>
Number of iterations you want to run the filter for.

<Conductance>
The value of the conductance term in anisotropic
diffusion filtering (Ex: 1.0)
Note: Large Conductance will oversmooth the image
It is important to tune the conductance to obtain
best results.

<Time Step>
This determines the step size in the gradient
descent. It can be atmost 0.0625.

<Filter Type>
Can Take 3 values:
0 means perform simple anisotropic diffusion

* - 1 means perform Chi-Squared smoothing (square the image and perform anisotropic diffusion and then subtract the variance of the noise, and take square root. (The square of a Rice distribution is a Chi Squared distribution with known bias equal to the variance of the noise) (Refer:Max likelihood Est. of Rician Ditribution Parameters. Sijbers et. al)
* - 2 means Perform Rician bias correction filtering.(Refer: Rician Noise Removal in DT-MRI.)
* - 3 is same as 2 except use a Gaussian Attachment Term .

<Sigma>
Estimate of noise in the data.
This can be done by squaring the airvoxels
in the real data. The sum of square of all
the intensities in the air region should equal
2*variance of the noise in the data.
(Sijbers et. al)

<lamda1, lamda2>
The weights for the Rician and Gaussian
attachment terms.

EXAMPLE
-------------
dwiFilter ../data/noisyDWI_10.nhdr filteredDWI.nhdr 1 1.0 0.0625 2 10 100 0

Filters the noisyDWI_10.nhdr for 1 iteration with a conductance of 1.0
timeStep 0.0625 using Rician filtering with a Rician attachement term
weight of 100. The estimate of noise in the input image is a sigma of 10
The filtered image is filteredDWI.nhdr.

===Tensor filtering===

Usage
--------------
tensorDiffuse <Arguments>
1. FilterType:(0-Euclidean, 1-Log Space,2-Riemannian)
2. numIterations:Iterations For Anisotropic Diffusion
3. timeStep:timeStep Used in Anisotropic Diffusion
4. conductance:Conductance used for Anisotropic Diffusion
5. Input (filename of input data)
6. Output (filename of output data)

Arguments 2,3,4 have the same meaning as described for dwiFilter (see above).

Argument 1 describes the filter type
* - 0: Euclidean Space filtering (tensors are treated as 6-d vectors)
* - 1: Log Space filtering (Fast and Simple Calculus on Tensors in the Log-Euclidean Framework. In J. Duncan and G. Gerig, editors, Proceedings of the 8th Int. Conf. on Medical Image Computing and Computer-Assisted Intervention - MICCAI 2005, Part I, volume 3749 of LNCS, Palm Springs, CA, USA, October 26-29, pages 115-122, 2005. Springer Verlag)
* - 2. Riemannian Space Filtering(A Riemannian Framework for the Processing of Tensor-Valued Images. In Ole Fogh Olsen, Luc Florak, and Arjan Kuijper, editors, Deep Structure, Singularities, and Computer Vision (DSSCV), number 3753 of LNCS, pages 112-123, June 2005. Springer Verlag.)

Currently, the Riemannian filter adjustment for negative eigen-values
is hard-coded in the source file.

Argument 5 is the name of the noisyTensor input.
Argument 6 is the name of the output tensor file

EXAMPLE
--------------
tensorFilter 2 1 0.0625 1.0 noisyTensor_10.nhdr FilteredTensor.nhrd

===Quick Tour of Features and Use===
List all the panels in your interface, their features, what they mean, and how to use them. For instance:

* '''Input panel:'''
* '''Parameters panel:'''
* '''Output panel:'''
* '''Viewing panel:'''

== Development ==

===Known bugs===

Follow this link to the Slicer3 bug tracker:

http://na-mic.org/Mantis/main_page.php

===Usability issues===

Follow this link to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing:

http://na-mic.org/Mantis/main_page.php

===Source code & documentation===

Customize following links for your module:

http://www.na-mic.org/ViewVC/index.cgi/

Links to documentation generated by doxygen:

http://www.na-mic.org/Slicer/Documentation/Slicer3/html/

== More Information ==

===Acknowledgement===
This work is part of the National Alliance for Medical Image Computing
(NAMIC), funded by the National Institutes of Health through the NIH Roadmap
for Medical Research, Grant U54 EB005149. Information on the National Centers
for Biomedical Computing can be obtained from http://nihroadmap.nih.gov/
bioinformatics. Funding for this work has also been provided by Center for
Integrative Biomedical Computing, NIH NCRR Project 2-P41-RR12553-07. We
thank Weili Lin and Guido Gerig from the University of North Carolina for
providing us with the DW-MRI data. Glyph visualizations created with Teem
(http://teem.sf.net).

===References===
Basu, S., Fletcher, P.T., Whitaker, R.T. Rician Noise Removal in Diffusion Tensor MRI. In Medical Image Computing and Computer Assisted Intervention (MICCAI), LNCS 4190, pp. 117-125, October, 2006.
[[http://www.sci.utah.edu/~fletcher/BasuDTIFilteringMICCAI2006.pdf | Paper link ]]