Diffusion Workflows

under construction

Importing DWI data:

There are import scripts for DWI DICOM data, as well as a specialized import script for our multi-shell, multi-band phase-encode-reversed diffusion imaging Siemens Prisma sequence.

Some definitions:

Multi-shell: Data with more than one non-zero b-value - e.g. our multi-shell data has Bvalues 0,1300,2600. Multi-band: accelerated multi-slice acquisition -> e.g. MB3 acquires 3 slices at a time, for 3x speedup Phase-encode reversed: Also known as blip-up blip-down, two identical DWI acquisitions, except different phase encode in each, e.g. L->R, R->L, used for effective correction of EPI distortions

##Three options:

importDicomDTI : For typical DWI, single phase-encode acquisition importDicomDTI_dcm2nii : Same thing, but an alternative if importDicomDTI fails

For EpLink Phase 2 data, use importMultiBandDTI: importMultiBandDTI <input DTI dicom folder blip 1> <phase encode line 1> <input DTI dicom folder blip 2> <phase encode line 2> .. 1. This imports two acquisitions to uncorrected folder 2. Performs topup to these and writes to distortCorrect folder

TODO: perhaps change name of importMultiBandDTI to importEpLinkMultiBandDTI

Preprocessing:

preprocDTI

1. Performs eddy-current correction (eddy_correct), and saves in the eddyCorrect folder
2. Distortion correction: a) IF a t1map exists, it runs non-rigid registration (distortCorrEPI) and saves results in distortCorrect folder b) IF a fieldmap exists, it runs fugue and saves results in distortCorrect folder
3. For each corrected copy (eddyCorrect, distortCorrect), it also runs bet and dtifit, to generate: brainmask.nii.gz dti_FA.nii.gz dti_L1.nii.gz dti_L2.nii.gz dti_L3.nii.gz dti_MD.nii.gz dti_MO.nii.gz dti_S0.nii.gz dti_V1.nii.gz dti_V2.nii.gz dti_V3.nii.gz

#FSL Probabilistic Tractography

bedpostProcess

1. Data is processed in distortCorrect if it exists, or eddyCorrect if not, and if neither exist it will quit
2. Copies necessary input files for bedpostx into: distortCorrect/bedpost (bvals bvecs data.nii.gz nodif_brain_mask.nii.gz)
3. Runs bedpostx, generating results in bedpost.bedpostX

bedpostTrackSeed <seed file - (nifti file, relative to your subj folder)>

If your seed was called: labels/dwi/HarvardOxford_bspline_f3d_rigid_aladin_MNI152_1mm/lthalamus.nii.gz

Runs probtrackx2 (probabilistic tracking) and save results in: bedpost.track.lthalamus

TO DO: bedpostTractography <config_file>

Tracking Config Files:

Tract config files are found in: $PIPELINE_CFG_DIR/tracts