#!/bin/bash

if [ $# -ne 1 ];
then

echo "Please provide path to working directory. E.g., $0 /Your/data/folder/ds001226-download"

else

dir=$1

for f in sub-PAT03
do

#run freesurfer recon-all on the T1w data
recon-all -i $dir/${f}/ses-preop/anat/${f}_ses-preop_T1w.nii.gz -s ${f}_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 $dir/freesurfer/${f}_recon/mri/aparc+aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt /imaging/local/software/mrtrix/v3.0.3_v2/share/mrtrix3/labelconvert/fs_default.txt $dir/${f}/ses-preop/dwi/${f}_fs_parcels.mif
 
#create the connectome
tck2connectome -symmetric -zero_diagonal -scale_invnodevol -tck_weights_in $dir/${f}/ses-preop/dwi/sift_10M.txt $dir/${f}/ses-preop/dwi/streamlines_10M.tck $dir/${f}/ses-preop/dwi/${f}_fs_parcels.mif $dir/${f}/ses-preop/dwi/${f}_fs_parcels.csv -out_assignment $dir/${f}/ses-preop/dwi/assignments_${f}_parcels.csv

done 

fi