#!/bin/bash
#
#SBATCH --ntasks=1
#SBATCH --mem-per-cpu=10000
#SBATCH --partition=pascalnodes
#SBATCH --time=12:00:00
#SBATCH --mail-type=FAIL
#SBATCH --mail-user=snolin@uab.edu
#SBATCH --job-name=FNstoV1tprob_%A_%a
#SBATCH --gres=gpu:1
#SBATCH --array=0-785%36
#SBATCH --out=/data/scratch/snolin/HCP_jobs/prob/FNstoV1tproblog_%A_%a.txt

#This scripts run FSL probtrackx from newcentral region of V1 to the Yeo parcellation of the frontoparietal network (net6), the mid-peripheral region of V1 to the cingulo opercular network (net4), and the far-peripheral region of V1 to the default mode network (net7).

#location of job scripts and logs
jobs=/data/scratch/snolin/HCP_jobs/prob

#set location for output of probtrackx paths
outp=/data/project/vislab/a/HCP_diff_Sara/FNstoV1tprob

#set location for where target lists will go
targ=$outp/targlists
mkdir $targ
#set location for where V1 segment labels exist
lab=/data/project/vislab/a/HCP_diff_Sara/subjects_reconall_postcheckcopy

#set location for where bedpostX directories are located
bed=/data/project/vislab/raw/HCP_900sub/HCP_diff_unzip_preproc

#location of participants you want to pull
diff=/data/project/vislab/a/HCP_diff_Sara/subjects_reconall_postcheck

FILES=(`ls -1 $diff`)
patient=${FILES[$SLURM_ARRAY_TASK_ID]}

#rename output file
ln $jobs/FNstoV1tproblog_${SLURM_ARRAY_JOB_ID}_${SLURM_ARRAY_TASK_ID}.txt $jobs/FNstoV1tproblog$patient.txt

for task in FP:newcentral:4 FP:mid:4 FP:newfar:4 CO:newcentral:6 CO:mid:6 CO:newfar:6 DMN:newcentral:7 DMN:mid:7 DMN:newfar:7
do
#parse task
network=`echo $task | cut -d: -f1`
V1=`echo $task | cut -d: -f2`
netnum=`echo $task | cut -d: -f3`

##network to V1###
#if [ -f $outp/${network}to${V1}/$patient/fdt_paths.nii.gz ]; then echo "${network}to${V1} has completed"
#else
#create folder structure
cd $outp
mkdir ${network}to${V1}
cd ${network}to${V1}
mkdir $patient

#create target list
cd $targ
touch targets${network}to${V1}_$patient.txt
echo "$lab/$patient/mri/${V1}V1_diffROI.nii" > targets${network}to${V1}_$patient.txt

#Probtrackx run on network to ${V1} V1
/share/apps/rc/software/FSL/5.0.9-centos6_64/bin/probtrackx2_gpu -x $lab/$patient/mri/net${netnum}_diffROI.nii -V 1 -l --onewaycondition -c 0.2 -S 2000 --steplength=0.5 -P 10000 --fibthresh=0.01 --distthresh=0.0 --sampvox=0.0 --forcedir --opd -s $bed/$patient/T1w/Diffusion.bedpostX/merged -m $bed/$patient/T1w/Diffusion.bedpostX/nodif_brain_mask --dir=$outp/${network}to${V1}/$patient --targetmasks=$targ/targets${network}to${V1}_$patient.txt --os2t
#fi
done
rm $jobs/FNstoV1tproblog_${SLURM_ARRAY_JOB_ID}_${SLURM_ARRAY_TASK_ID}.txt