• FSL's Diffusion Toolbox

• 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.
  • runBEDPOST_PRE.sh – sets up the bedpostx directory
  • submit_CROSS.sh – submits the individual slices through runBEDPOST_CROSS.sh (this does not need to be run)
  • 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

• copy the dti.bedpostx folder to the subject's folder on Cohen
• now dti can be normalized and dyads can be masked: post_dti_steps.sh
• navigate to /data/code and run it as bash -x post_dti_steps.sh SUBJNUM

• Convert the raw anatomicals into nifti, and flip them from the default orientation into LAS (FSL's preferred orientation) - script
• Run the FIRST subcortical segmentation - FIRST Methods - FSL FIRST Documentation
• Run FreeSurfer segmentation on the same T1 as FIRST - FreeSurfer Methods - FreeSurfer Documentation
• Calculate Overlap using fslstats - Overlap Methods