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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 | ||
| + | #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 | ||
| + | # | ||
| − | |||
| − | + | == Next steps:== | |
| + | #T-con November 16th 2 PM EST/ noon MST Agenda items include feedback on sample data set & ROIs | ||
| + | #Next face to face gathering will be at the AHM, Randy to schedule time on the agenda t continue this project | ||
| + | #Proper implementation of DTI gradient orientation system in ITK, nrrd, TEEM, etc (Casey/Tom to file bug report, bring it up in an upcoming Engineering T-con, plan for work on it next Project week)) | ||
Latest revision as of 05:21, 4 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) 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
Next steps:
- T-con November 16th 2 PM EST/ noon MST Agenda items include feedback on sample data set & ROIs
- Next face to face gathering will be at the AHM, Randy to schedule time on the agenda t continue this project
- Proper implementation of DTI gradient orientation system in ITK, nrrd, TEEM, etc (Casey/Tom to file bug report, bring it up in an upcoming Engineering T-con, plan for work on it next Project week))
