Difference between revisions of "ActionPlan"
RandyGollub (talk | contribs) (New page: Comparative analysis of tractography methods/approaches #General Taxonomy (based on ROI requirements)- use all those presented at this conference and FSL tool #Reproducibility of tractogr...) |
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Comparative analysis of tractography methods/approaches | Comparative analysis of tractography methods/approaches | ||
#General Taxonomy (based on ROI requirements)- use all those presented at this conference and FSL tool | #General Taxonomy (based on ROI requirements)- use all those presented at this conference and FSL tool | ||
| − | |||
#Reproducibility of tractography approaches | #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. | #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 | + | 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) 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 | ||
| − | + | *Outcome metrics: | |
| − | + | Space carved (Casey's DTIprocess tool that generates a volume label map measure from traceline) in high resolution. Use this for test-retest metric | |
| − | |||
Revision as of 17:28, 2 October 2007
Home < ActionPlanComparative 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) 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
- Outcome metrics:
Space carved (Casey's DTIprocess tool that generates a volume label map measure from traceline) in high resolution. Use this for test-retest metric
