2013 Summer Project Week:DWIConvert

2013-06-17T16:54:35Z

Kentwilliams:

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

==Key Investigators==
* UIowa: Kent Williams, esqr.

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

<h3>Objective</h3>
Improve the DICOM - DWI conversion mechanism in Slicer to support more scanners and file output formats.

<h6> Specific goals </h6>
#Working with the PREDICT and HDNI longitudinal data sets as sample multi-site, multi-scanner test data corpus, add support for more scanning protocols and software versions.
#General code clean-up -- DicomToNrrd had been repeatedly modified over the past few years by multiple authors, to the point where there is many instances of 'dead' code (never executed) and confusing paths of execution.

</div>

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

<h3>Approach, Plan</h3>
#Approach
##Begin with original DicomToNrrd code.
##Analyze source code to capture the implicit knowledge about DWI DICOM data sets.
##Refactor code to straighten out program logic and remove obsolete and incorrect code.
#Plan
##Incrementally refactor and improve C++ code
##Use regression tests, and tests against large collections of DICOM data sets to validate code
##Incorporate program into BRAINSTools suite (hosted at github) to facilitate inclusion in Slicer.
##Work with Slicer community to come up with new 'problem' datasets for testing.
</div>

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

<h3>Progress</h3>
#Siemens scanner models supported: Avanto, Espree, Sonata, Symphony, SymphonyTim, TrioTim, Verio
#GE scanner models supported: GENESIS_SIGNA, SIGNA, SIGNA EXCITE,SIGNA HDx, Signa HDxt
#Philips scanner models supported: Achieva, Intera
#Added support for Hitachi scanners -- in progress.
#Refactored original monolithic code into a collection of classes, one per scanner manufacturer, with common code isolated from scanner-specific code.
#More modular structure makes it easier to add new scanner models.
</div>
</div>

==Delivery Mechanism==

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

# Part of BRAINSTools suite https://github.com/BRAINSia/BRAINSTools
#Slicer Module
##Built-in YES
##Extension -- commandline
##Extension -- loadable

==References==

2012 Summer Project Week:DicomToNrrd

2012-06-07T20:02:04Z

Kentwilliams:

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

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

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

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

</div>

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

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

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

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

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

</div>

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

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

==Delivery Mechanism==

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

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

==References==

NAMIC Wiki - User contributions [en]

2013 Summer Project Week:DWIConvert

2012 Summer Project Week:DicomToNrrd