Difference between revisions of "2013 Summer Project Week:DWIConvert"

From NAMIC Wiki
Jump to: navigation, search
m (Fix table formatting discovered while converting to GitHub Flavored Markdown using pandoc (through https://github.com/outofcontrol/mediawiki-to-gfm))
Tag: 2017 source edit
 
(10 intermediate revisions by 3 users not shown)
Line 2: Line 2:
 
<gallery>
 
<gallery>
 
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
 
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
−
Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.
 
−
Image:genuFA.jpg|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.
 
 
</gallery>
 
</gallery>
−
 
+
[[2013_Summer_Project_Week#Agenda|Back to Summer project week Agenda]]
−
2013_Summer_Project_Week:DWIConvert
 
−
 
 
 
==Key Investigators==
 
==Key Investigators==
−
* UNC: Isabelle Corouge, Casey Goodlett, Guido Gerig
+
* UIowa: Kent Williams, esqr.
−
* Utah: Tom Fletcher, Ross Whitaker
 
  
 
<div style="margin: 20px;">
 
<div style="margin: 20px;">
Line 16: Line 11:
  
 
<h3>Objective</h3>
 
<h3>Objective</h3>
−
We are developing methods for analyzing diffusion tensor data along fiber tracts. The goal is to be able to make statistical group comparisons with fiber tracts as a common reference frame for comparison.
+
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>
Line 28: Line 22:
  
 
<h3>Approach, Plan</h3>
 
<h3>Approach, Plan</h3>
−
 
+
#Approach
−
Our approach for analyzing diffusion tensors is summarized in the IPMI 2007 reference below. The main challenge to this approach is <foo>.
+
##Begin with original DicomToNrrd code.
−
 
+
##Analyze source code to capture the implicit knowledge about DWI DICOM data sets.
−
Our plan for the project week is to first try out <bar>,...
+
##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>
  
Line 38: Line 36:
  
 
<h3>Progress</h3>
 
<h3>Progress</h3>
−
Software for the fiber tracking and statistical analysis along the tracts has been implemented. The statistical methods for diffusion tensors are implemented as ITK code as part of the [[NA-MIC/Projects/Diffusion_Image_Analysis/DTI_Software_and_Algorithm_Infrastructure|DTI Software Infrastructure]] project. The methods have been validated on a repeated scan of a healthy individual. This work has been published as a conference paper (MICCAI 2005) and a journal version (MEDIA 2006). Our recent IPMI 2007 paper includes a nonparametric regression method for analyzing data along a fiber tract.
+
* 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>
 
</div>
 +
<div style="width: 85%; float: center;">
 +
{| class="wikitable"
 +
! Scanner
 +
Manufacturer
 +
! Software version
 +
|-
 +
| Seimans
 +
| Avanto<br/>Espree<br/>Sonata<br/>Symphony<br/>SymphonyTim<br/>TrioTim<br/>Verio
 +
|-
 +
| GE
 +
| GENESIS_SIGNA<br/>SIGNA<br/>SIGNA EXCITE<br/>SIGNA HDx<br/>Signa HDxt
 +
|-
 +
| Philips
 +
| Achieva<br/>Intera
 +
|-
 +
| Hitachi
 +
| style="font-style: italic; color: red;" | In Progress
 +
|}
 
</div>
 
</div>
  
Line 48: Line 64:
 
This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)
 
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
+
# Part of BRAINSTools suite https://github.com/BRAINSia/BRAINSTools
 
#Slicer Module
 
#Slicer Module
−
##Built-in
+
##Built-in YES
 
##Extension -- commandline
 
##Extension -- commandline
 
##Extension -- loadable
 
##Extension -- loadable
−
#Other (Please specify)
 
  
 
==References==
 
==References==
−
*Fletcher P, Tao R, Jeong W, Whitaker R. [http://www.na-mic.org/publications/item/view/634 A volumetric approach to quantifying region-to-region white matter connectivity in diffusion tensor MRI.] Inf Process Med Imaging. 2007;20:346-358. PMID: 17633712.
 
−
* Corouge I, Fletcher P, Joshi S, Gouttard S, Gerig G. [http://www.na-mic.org/publications/item/view/292 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Med Image Anal. 2006 Oct;10(5):786-98. PMID: 16926104.
 
−
* Corouge I, Fletcher P, Joshi S, Gilmore J, Gerig G. [http://www.na-mic.org/publications/item/view/1122 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Int Conf Med Image Comput Comput Assist Interv. 2005;8(Pt 1):131-9. PMID: 16685838.
 
−
* Goodlett C, Corouge I, Jomier M, Gerig G, A Quantitative DTI Fiber Tract Analysis Suite, The Insight Journal, vol. ISC/NAMIC/ MICCAI Workshop on Open-Source Software, 2005, Online publication: http://hdl.handle.net/1926/39 .
 

Latest revision as of 04:25, 11 April 2023

Home < 2013 Summer Project Week:DWIConvert
Back to Summer project week Agenda

Key Investigators

  • UIowa: Kent Williams, esqr.

Objective

Improve the DICOM - DWI conversion mechanism in Slicer to support more scanners and file output formats.

Specific goals
  1. 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.
  2. 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.

Approach, Plan

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

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.
Scanner

Manufacturer

Software version
Seimans Avanto
Espree
Sonata
Symphony
SymphonyTim
TrioTim
Verio
GE GENESIS_SIGNA
SIGNA
SIGNA EXCITE
SIGNA HDx
Signa HDxt
Philips Achieva
Intera
Hitachi In Progress

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)

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

References

Retrieved from "https://www.na-mic.org/w/index.php?title=2013_Summer_Project_Week:DWIConvert&oldid=98827"