• 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

• CreateDiff
• MultDiff
• ScanDiff
• ResliceDiff
• SplitDiff
• CombineDiff

DTI processing

• ComputeSingleTensor
• TensorEig
• TensorIndices
• FiberTrack
• DTIregressStats

UCF utilities

• UcfHistogram
• UcfRoiSelector
• UcftoAnz
• UCFlengthSelector

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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