#!/bin/bash


#run freesurfer recon-all on the T1w data
recon-all -i sub-CON03/ses-preop/anat/sub-CON03_ses-preop_T1w.nii.gz -s sub-CON03_recon -all

#convert freesurfer labels to mrtrix format
#NOTE: you must replace the path to the fs_default.txt file below to match the path to your mrtrix3 installation
labelconvert freesurfer/sub-CON03_recon/mri/aparc+aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt /imaging/local/software/mrtrix/v3.0.3_v2/share/mrtrix3/labelconvert/fs_default.txt sub-CON03/ses-preop/dwi/sub-CON03_fs_parcels.mif -force
 
#create the connectome
tck2connectome -symmetric -zero_diagonal -scale_invnodevol -tck_weights_in sub-CON03/ses-preop/dwi/sift_10M.txt sub-CON03/ses-preop/dwi/streamlines_10M.tck sub-CON03/ses-preop/dwi/sub-CON03_fs_parcels.mif sub-CON03/ses-preop/dwi/sub-CON03_fs_parcels.csv -out_assignment sub-CON03/ses-preop/dwi/assignments_sub-CON03_parcels.csv -force