Trying to get ASLPrep to Work

src/aslprep-pre.sh

@@ -8,25 +8,20 @@ export m0scan=NO_M0SCAN
 export aslscan=NO_ASLSCAN
 export aslsource=NO_ASLSOURCE
 export examcard=NO_EXAMCARD
+export t1scan=NO_T1SCAN
 
 # Parse options
 while [[ $# -gt 0 ]]; do
   key="${1}"
   case $key in
-    --indir)
-      export indir="${2}"; shift; shift ;;
-    --outdir)
-      export bidsdir="${2}"; shift; shift ;;
-    --m0scan)
-      export m0scan="${2}"; shift; shift ;;
-    --aslscan)
-      export aslscan="${2}"; shift; shift ;;
-    --sourcescan)
-      export sourcescan="${2}"; shift; shift ;;
-    --examcard)
-      export examcard="${2}"; shift; shift ;;
-    --fs_license)
-      export fs_license="${2}"; shift; shift ;;
+    --indir)        export indir="${2}";        shift; shift ;;
+    --outdir)       export bidsdir="${2}";      shift; shift ;;
+    --m0scan)       export m0scan="${2}";       shift; shift ;;
+    --aslscan)      export aslscan="${2}";      shift; shift ;;
+    --sourcescan)   export sourcescan="${2}";   shift; shift ;;
+    --examcard)     export examcard="${2}";     shift; shift ;;
+    --fs_license)   export fs_license="${2}";   shift; shift ;;
+    --t1scan)       export t1scan="${2}";       shift; shift ;;
     *)
       echo Unknown input "${1}"; shift ;;
   esac
@@ -35,10 +30,10 @@ done
 
 # Format BIDS directory and convert to nii
 # Save Series Description to json
-organize_data.py -i ${indir} -a ${aslscan} -m ${m0scan} -s ${sourcescan}
+organize_data.py -i ${indir} -a ${aslscan} -m ${m0scan} -s ${sourcescan} -t ${t1scan}
 
 #Get necessary data form examcard and write to json sidecar
 examcard2json.py -i ${indir} -b ${bidsdir} -e ${examcard}
 
 #Create ASL context tsv file
-create_context_tsv.py -b ${bidsdir}
+create_tsv.py -b ${bidsdir}

src/bash_commands.sh

@@ -0,0 +1,21 @@
+#!/bin/bash
+
+export indir=$1
+export source=$2
+export m0=$3
+export t1w=$4
+export source_base=$5
+export m0_base=$6
+export t1w_base=$7
+
+# move scans to BIDS directories
+mkdir -p $indir/BIDS/sub-01/ses-01/anat/
+mkdir -p $indir/BIDS/sub-01/ses-01/perf/
+
+cp $source $indir/BIDS/sub-01/ses-01/perf/$source_base
+cp $m0 $indir/BIDS/sub-01/ses-01/perf/m0$m0_base
+cp $t1w $indir/BIDS/sub-01/ses-01/anat/$t1w_base
+
+# run dcm2niix on source and m0 scans
+/data/mcr/centos7/dcm2niix/v1.0.20240202/console/dcm2niix -z y -f %b $indir/BIDS/sub-01/ses-01/anat
+/data/mcr/centos7/dcm2niix/v1.0.20240202/console/dcm2niix -z y -f %b $indir/BIDS/sub-01/ses-01/perf

src/create_tsv.py

@@ -0,0 +1,65 @@
+#!/usr/bin/env python
+
+'''
+Inputs:
+    -b: BIDS file structure containing nifti files and json sidecars
+Outputs:
+    updated json sidecar for ASL images in Exam Card
+        Name: sub-01_ses-01_asl.json OR sub-01_ses-01_m0scan.json
+'''
+
+from __future__ import print_function
+import os
+import csv
+import sys, getopt
+import glob
+import nibabel as nib
+
+def main(argv):
+    bids = ''
+    try:
+        opts, args = getopt.getopt(argv, "hb:",["bids="])
+    except getopt.GetoptError:
+        print('create_tsv.py -b <folder>')
+        sys.exit(2)
+
+    for opt, arg in opts:
+        if opt == '-h':
+            print('create_tsv.py -b <folder>')
+            sys.exit()
+        elif opt in ("-b", "--bids"):
+            bids = arg
+
+    print('BIDS Folder: ', bids)
+
+    asl_file = glob.glob(bids+'/sub-*/ses-*/perf/*_asl.nii.gz')
+
+    print(asl_file)
+    print(asl_file[0])
+
+    if asl_file:
+        asl_img = nib.load(asl_file[0])
+        if len(asl_img.shape) < 4:
+            print('ASL data not 4-dimensional. Please repeat with correct file.')
+            sys.exit()
+        else:
+            abs_path = os.path.abspath(asl_file[0])
+            file_struct = abs_path.split('/')
+            tsv_loc = '/'.join(file_struct[:-1]) + ''
+            name_struct = file_struct[-1].split('_')
+            tsv_name = '_'.join(name_struct[:-1]) + '_aslcontext.tsv'
+
+            with open(tsv_loc + '/' + tsv_name,'wt') as tsv_file:
+                csv_writer=csv.writer(tsv_file,delimiter='\t')
+                csv_writer.writerow(['volume_type'])
+                for x in range(asl_img.shape[3]):
+                    if (x % 2) == 0:
+                        csv_writer.writerow(['control'])
+                    else:
+                        csv_writer.writerow(['label'])
+    else:
+        print('Files not found or data is not in BIDS format. Please repeat with correct file/structure.')
+        sys.exit()
+
+if __name__ == '__main__':
+    main(sys.argv[1:])