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Comparative analysis of tractography methods/approaches
#General Taxonomy (based on ROI requirements)- use all those presented at this conference and FSL tool
#Reproducibility of tractography approaches
#Our same 5 ROIs + CC.  Sonia and Randy to make first pass in 1 subject, validate with Marek's lab and then send around to be sure work with algorithms.

Need data sets, appropriate ROIs.  Iterate beginning with n=1 for ROI generation.

Exploration of potential data sets (UNC n=1, 10 acquisitions with 6 directions; MIND n=10, 8 acquisitions, 2x at each of 3 sites with 6 directions and 2x at 1 site with 60 directions).

Sylvain volunteers to make nrrd headers for the 10 MIND subjects data from MGH test/retest with Jeremy, Vince, Randy.

Outcome metrics
#User interface, hardware/software (processor speed, platform, RAM), operator time

== Preprocessing stream: ==
#DWI with NiFTY header + gradient directions 
#Field Map correction (NMN.Iowa.MGH) if we verify that this is helpful
#Eddy Current Correction  (affine registration) (BWH)
#nrrd (BWH) 
#weighted least squares (FSL won't match on this step) tensor estimation using #TEEM library (BWH)
#T1 white matter mask co-registered to Eddy current corrected DWI data (NA-MIC affine registration tool) (Freesurfer white matter + ?  vs. EMSegmentation- Sonia/Sylvain) 
#ROIs in DWI/DTI space
#Affine registration transformation to bring retest into test space (use this for mapping ROIs and outcome label maps only from test to retest for each subject)


== Outcome metrics: ==
#Space carved (Casey's DTIprocess tool that generates a volume label map measure from traceline).  This will give volumes, overlap, mean and Std Dev of FA, trace, mode.  Use these for test-retest metrics.  Pass these label maps to Sonia she will generate these.
#Casey's FiberCompare multiple traceline visualization tool
#Staple method to find common agreement (specificity and sensitivity)
#Further discussion of how best to parameterize tracts at January AHM
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