Loop_probtrax_EachSeedtoEachTarget.sh

#!/bin/bash

#supply a seeds.txt and a targets.txt file located in each subject's folder in /YOUR_BEDPOST_DIR/CoRegistration/ that gives #path to a set of seeds and targets in patient diffusion space.

homepath=/YOUR_HOME(ALLsubjects)_DIRECTORY/
cd $homepath

transform3=/YOUR_RIGID_TRANSFORM_IITFA_to_MNI.mat
transform4=/YOUR_AFFINE_TRANSFORM_IITFA_to_MNI.mat
transform5=/YOUR_NONLINEAR_WARP_IITFA_to_MNI.nii.gz

for d in $homepath/* #loop through all control scans
do
    cd $homepath/$d/YOUR_BEDPOST_DIR 
        #make post txform target directories
        mkdir probtrax
        mkdir -p probtrax/specific_targets
        
        #assign relevant txform files
        reference=/YOUR_REF_BRAIN.nii.gz
        transform1=/YOURSUBJ_to_IIT_affine_transform.mat
        transform2=/YOURSUBJ_TO_IIT_nonlinear_warp.nii.gz
        
        #do probtrackx2
        while read p
        do
          #get the name of the seed we're using for the output directory
      seedname=`echo $p`
      #Get total number of paths emanating from seed. 5000*voxel#
          max=`fslstats $p -V | awk -F ' ' '{print $1}'`
          max_paths=`echo "$((5000 *$max))"`
        
      #save SEED max_paths into appropriate file
          echo $max_paths >> /DATA_OUTPUT_FOLDER/max_paths_SEED.txt

        while read a  
               do
                #get target name
                targetname=`echo $a`
          #get the total number of paths that emanate from target, when used as a seed.
                maxTarget=`fslstats $a -V | awk -F ' ' '{print $1}'`
                max_paths_Targ=`echo "$((5000 *$maxTarget))"`
                #save TARGET max_paths into appropriate file
                echo $max_paths_Targ >> /DATA_OUTPUT_FOLDER/max_paths_Targ.txt    
           
           ##Waypoint calculation, using callosal exclusion, stop mask, A:B calculation
            probtrackx2 -s bedpost_dir.bedpostX/merged -m bedpost_dir.bedpostX/nodif_brain_mask.nii.gz -x $p -- 
            dir="$seedname"_"$targetname"_termmask --waypoints=$a --stop=$a --avoid=CoRegistration/CORPUSCALLOSUM.nii.gz -l -c 
            0.2 -S 2000 --steplength=0.5 -P 5000 --fibthresh=0.01 --distthresh=0.0 --sampvox=0.0 --opd -V 1
                  
            #save waytotal number into variable, move resulting probtrax folder into appropriate directory
                  waytotalX=$(head -n 1 *$targetname*/waytotal)
            
            #make a normalized paths file for brining to MNI space
                fslmaths *$targetname*/fdt_paths.nii.gz -div $max_paths fdt_paths_normalized.nii.gz
                mv *normalized* *$targetname*
            #move folder into subject specific subdirectory
                  mv *$targetname* probtrax/specific_targets
        
               ##Waypoint calculation, using callosal exclusion, stop mask, B:A calculation, store waytotal as variable, move 
            resulting probtrax folder into appropriate directory    
            probtrackx2 -s bedpost_dir.bedpostX/merged -m bedpost_dir.bedpostX/nodif_brain_mask.nii.gz -x $a -- 
            dir="$targetname"_"$seedname"_termmask --waypoints=$p --stop=$p --
            avoid=CoRegistration/MNIvolumes_WarpedTo_SubjDiff/WM_Callosal_Body_MNI_Juelich_thresh40_DiffSpace.nii.gz -l -c 0.2 
            -S 2000 --steplength=0.5 -P 5000 --fibthresh=0.01 --distthresh=0.0 --sampvox=0.0 --opd -V 1
            
            #save waytotal number into variable, move resulting probtrax folder into appropriate directory
                  waytotalB=$(head -n 1 *$targetname*/waytotal)
                  mv *$targetname* probtrax/specific_targets
    

                #warp seed to target paths into MNI space
                $ANTSPATH/antsApplyTransforms -d 3 -i probtrax/specific_targets/"$seedname"_"$targetname"_termmask/fdt_paths_normalized.nii.gz -r $reference -o       
            /YOUR_SUBJ_MNI_OUTPUTDIR/"$seedname"_"$targetname"_MNIpaths.nii.gz -t $transform5 -t       
            $transform4 -t $transform3 -t $transform2 -t $transform1 -v
        

        
            #store waytotal values into signle textfile
            echo $waytotalX >> /DATA_OUTPUT_FOLDER/waytotals.txt
            echo $waytotalB >> $homepath/sbsnider/response_processing/waytotalsBtoA.txt
              done <CoRegistration/targets.txt
            
          done < CoRegistration/seeds.txt


      cd $homepath


done