Iowa-NA-MIC-2010-Kickoff - Revision history

Hjmjohnson: /* DTI Processing */

2010-10-27T15:08:29Z

DTI Processing

2010-10-25T21:21:29Z

BatchMake Processing and Grid Wizard

2010-10-25T21:05:42Z

Shape Analysis

2010-10-25T20:34:53Z

DTI Processing

2010-10-25T20:05:35Z

DTI Processing

2010-10-25T19:46:30Z

Data

2010-10-25T19:40:26Z

Data

2010-10-25T19:34:18Z

Shape Analysis

2010-10-25T19:32:56Z

Data

2010-10-25T19:13:25Z

Shape Analysis

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 *Two major areas: DTI processing and shape analysis
 *Marco Ruiz,  integration of XNAT with GridWizard to allow XNAT pipeline access to external computational resources
 === DTI Processing ===
 Goals: Tools for a longitudinal analysis pipeline of changes measured by fiber tractography to identify white matter tracts that have strong co-morbid degenerative timelines compared to subcortical degeneration over time. Enable the use of the advanced DTI processing in NA-MIC within PREDICT HD. Specifically, adapt all NA-MIC tools to work as individual external Slicer modules (in part they already exist, but need further work), as well as combine them into a single Slicer DTI processing wizard.
 Steps/Modules:
 * Process data from raw DICOM data (enhanced DicomToNRRDConverter)
 ** 2010-11-30 (Mark, Joy): Add testing data suite to DicomToNRRDConverter  (Joy to identify, Mark to implement)

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 ** 2011-06-24 (Marco): Distribute from local data repositories.
 ** 2012-06-24 (Marco/Kevin Archie/Tim Olsen): Distribute from XNAT
 === Data ===

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 Steps/Modules:
-* Individual SPHARM tools (exists, needs polishing)
+* 2011-04-01 (Slicer Team/Core2):Sun Grid Engine compatibility
-* SPHARM shape summary tool (exists, needs polishing)
+* 2011-04-01 (Clement): Clean up existing tools for deployment at Iowa
-* Add support for particle shape analysis (new Slicer module)
+** Individual SPHARM tools (exists, needs polishing)
-* Sun Grid Engine compatibility
+** SPHARM shape summary tool (exists, needs polishing)
 ** Target of 2011-01-14:  have feasibility shape analysis done to identify outstanding work that needs to be done.
 === Data ===

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 ** Loading reports so that batch processing mode and gui processing mode allow the same user
 ** GUI should allow for manual individual rejection of DWI gradients
-* DTI estimation, property map generation (existing Slicer modules)
+* 2011-12-31 (Clement/Mark): DTI estimation, property map generation (existing Slicer modules)
+** Review and make command line interfaces and make a dictionary of common command line arguments across the tool sets.
-* DTI atlas registration (new Slicer module)
+** Push DTIProcess tools into full Slicer Modules
-* DTI atlas based fiber analysis (new Slicer module)
+* 2011-08-15 (Clement): DTI atlas registration (new Slicer module)
-* DTI atlas computation module (new Slicer module)
+** Investigate if both scalars and higher models can both be supported.
-* DWI atlas mapping tool (new Slicer module)
+** Investigate DTITK inclusion Slicer3
-* Appropriate reporting of all steps
+* 2012-05-01 (Clement): DTI atlas based fiber analysis (new Slicer module)
-* DTI processing wizard in Slicer
+** Tools need re-writing to make them slicer3 compatible.
-* Longitudinal DTI analysis module
+* 2012-07-01 (Clement): DTI atlas computation module (new Slicer module)
-* Fiber profile measurement/visualization within Slicer
+** NITRC implementation FRAT needs rewrite with new greedy registration methods
 === Shape Analysis ===

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 Steps/Modules:
-* process data from raw DICOM data (enhanced DicomToNRRDConverter)
+* Process data from raw DICOM data (enhanced DicomToNRRDConverter)
-* DTI noise estimation, Rician noise filtering
+** 2010-11-30 (Mark, Joy): Add testing data suite to DicomToNRRDConverter  (Joy to identify, Mark to implement)
-* DTI QC and motion/eddy current correction (enhanced DTIPrep)
+** Target 2010-12-31(Mark): CMake URL data download mechanisms (Look at Titan CMake has examples of this).
 * DTI estimation, property map generation (existing Slicer modules)
 * DTI atlas registration (new Slicer module)
 * DTI atlas based fiber analysis (new Slicer module)

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 ** Will need to run auto-workup for generating Caudate/putamen/hippocampus/thalmus masks.
 ** Data exchange will be done through XNAT.  including derived data.
 == Outreach ==

← Older revision		Revision as of 19:32, 25 October 2010
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	*Yes. Over 2900 scan sessions collected. We will need to identify the meaningful subset of this data, get final approval from the Predict Steering Committee for that subset,and then re-deidentify it and post to XNAT for NA-MIC purposes.		*Yes. Over 2900 scan sessions collected. We will need to identify the meaningful subset of this data, get final approval from the Predict Steering Committee for that subset,and then re-deidentify it and post to XNAT for NA-MIC purposes.
		+	* (Target date of 2010-12-10) Identified the FMRI_024 data (77 subjects, 2-3 years longitudinal) as a good candidate data set for collaborative algorithm development platform. This data set has 3 71direction+8B0 DTI data sets, 2 1.0^3 T1 data sets, and a 0.56x0.56x1.4 T2 data set.
		+	** Will likely need to collect clinical data for shape analysis work that includes: (Age, Gender, Dx, Burdon Score, Motor Score).
		+	** Will need to re-de-identify all the data to be used here.
		+	** Will need to run auto-workup for generating Caudate/putamen/hippocampus/thalmus masks.

	== Outreach ==		== Outreach ==