- Name: Kristi Clark
- Login Name: kclark
- Email: kaclark@ucla.edu
- Department: Neurology
- Location: Brain Mapping Center 237
- Comment: Source code & binaries were updated May 1, 2009 to fix a bug in the fiber tracking algorithm. The bug caused the program to terminate early under special conditions. So if you have fiber tracking results that were generated using the previous version of the algorithm, there may be false negatives, but not false positives.
DTI Documents
Getting started/Overview powerpoint:
BasicDTIanalysis_howto.ppt
KClark_LONI_DTI_Suite.ppt: Talk from July 30, 2009: overview of tools and their use in the pipeline
LONI DTI Suite Modules
- modules.pipe: A compilation of all LONI DTI Suite modules in a single pipeline.
To download the modules.pipe, right click & "save link as"
LONI DTI Suite Work Flows
To download the flows, right click & "save link as"
1. Getting started (convert data from DICOM to analyze, correct gradient table for slice prescription, generate .diff file and/or bvals/bvecs for FSL):
correct_slice_prescription.pipe
2a. Correct for eddy current induced distortions & motion artifacts:
dti_eddy_motion.pipe
2b. Correct for eddy current induced distortions & motion artifacts using data with two repeats (slightly more complicated):
dti_eddy_motion_datawith2repeats.pipe
3. DTI analysis, a collection of tools to estimate the tensor, tensor-derived scalar metrics (MD, FA, etc.), regression statistics to evaluate the fit of the tensor model at each voxel, and streamline tractography:
DTI_analysis.pipe
4. Use an atlas ROI approach to compute mean DTI-derived metric, e.g. FA:
atlas_based_ROI_analysis_for_dti_data.pipe
5. Tractography options:
tractography_options.pipe
6. Use an atlas ROI approach to do tractography:
atlas_based_tractography.pipe
LONI DTI Suite
Click each filename for a description & help file
Creation and manipulation of .diff files
DTI processing
UCF utilities
LONI DTI Suite: Example Analysis
Example 1 step 1: convert DICOM to ANZ, build a .diff, 6-direction data, 4 repeats, b=1100:
example1_step1.pipe
Example 1, finish: compute the mean FA for the left superior longitudinal fasciculus, using an atlas approach:
example1_finish.pipe
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Related topics
Attachment  | Action | Size | Date | Who | Comment |
BasicDTIanalysis_howto.ppt | manage | 5947.0 K | 19 Jul 2008 - 08:18 | KristiClark | Powerpoint tutorial |
DTI_analysis.pipe | manage | 320.9 K | 19 Jul 2008 - 07:50 | KristiClark | Compute tensor, eigenvectors, eigenvalues, fiber tractography, etc. |
testdata.tar.gz | manage | 21140.1 K | 19 Jul 2008 - 13:33 | KristiClark | Test dataset 30 directions |
dti_tools_source_code.tar | manage | 2890.0 K | 03 May 2009 - 18:43 | KristiClark | Source code |
linux_binaries.tar | manage | 25230.0 K | 03 May 2009 - 18:49 | KristiClark | Code compiled for linux |
correct_slice_prescription.pipe | manage | 244.6 K | 22 Jul 2008 - 23:49 | KristiClark | Reconstruct data and correct slice prescription |
dti_eddy_motion.pipe | manage | 150.6 K | 22 Jul 2008 - 23:49 | KristiClark | Correct for eddy current induced distortions & motion artifacts |
modules.pipe | manage | 700.7 K | 30 Jul 2009 - 04:05 | KristiClark | A compilation of all LONI DTI Suite modules in a single pipeline. |
atlas_based_ROI_analysis_for_dti_data.pipe | manage | 233.6 K | 30 Jul 2009 - 04:28 | KristiClark | Use an atlas ROI approach to compute mean DTI-derived metric, e.g. FA |
dti_eddy_motion_datawith2repeats.pipe | manage | 161.4 K | 30 Jul 2009 - 04:19 | KristiClark | An example of how to do dti_eddy_motion for data with two repeats. |
tractography_options.pipe | manage | 89.3 K | 30 Jul 2009 - 04:20 | KristiClark | Tractography options |
atlas_based_tractography.pipe | manage | 261.1 K | 30 Jul 2009 - 04:33 | KristiClark | Use an atlas ROI approach to do tractography |
example1_step1.pipe | manage | 204.4 K | 30 Jul 2009 - 04:36 | KristiClark | Example 1 step 1: convert DICOM to ANZ, build a .diff, 6-direction data, 4 repeats, b=1100 |
example1_finish.pipe | manage | 603.2 K | 30 Jul 2009 - 04:37 | KristiClark | Example 1, finish: compute the mean FA for the left superior longitudinal fasciculus, using an atlas approach |
KClark_LONI_DTI_Suite.ppt | manage | 4063.0 K | 30 Jul 2009 - 21:07 | KristiClark | Talk from July 30, 2009: overview of tools and their use in the pipeline |