mirecc:mireccanat
DTI processing
convert the raw DTI data into nifti format
skull strip the DTI
run eddy current correction
run dtifit to calculate FA,eigenvalues,etc
these steps are handled through the
make_dti script
run bedpostx on the cluster to estimate crossing fibers
running bedpost requires copying the dtifit results to a temporary directory within the MIRECC.03/Analysis/dti_temp folder and running each slice individually through the cluster. If you do not run the slices individually they are run sequentially, which can take 1 week to finish.
-
-
once all 60+ slices are completed, they need to be combined into one volume and moved back to the individual subject's directory.
navigate to the subject's folder (on Selye) and run:
bedpostx_postproc.sh dti
First, FreeSurfer, Manual Comparison
Convert the raw anatomicals into nifti, and flip them from the default orientation into LAS (FSL's preferred orientation) -
script
-
-
-
flowchart showing steps of getting first/freesurfer volumes into the same space
mirecc/mireccanat.txt · Last modified: 2023/02/23 18:43 (external edit)