slicetiming

VUIIS · Mar 12, 2024 · 33e65c0 · 33e65c0
1 parent defd977
commit 33e65c0
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Showing 2 changed files with 63 additions and 22 deletions.
diff --git a/src/fmriprep-prep.sh b/src/fmriprep-prep.sh
@@ -7,6 +7,7 @@ export t1_niigz=/INPUTS/t1.nii.gz
 export fmri_niigzs=/INPUTS/fmri.nii.gz
 export rpefwd_niigz=""
 export rperev_niigz=""
+export slicetiming=""
 export bids_dir=/INPUTS/BIDS
 export sub=01
 export ses=01
@@ -24,6 +25,7 @@ while [[ $# -gt 0 ]]; do
         --bids_dir)       export bids_dir="$2";       shift; shift ;;
         --sub)            export sub="$2";            shift; shift ;;
         --ses)            export ses="$2";            shift; shift ;;
+        --slicetiming)    export slicetiming="$2";    shift; shift ;;
         --fmri_niigzs)
             next="$2"
             while ! [[ "$next" =~ -.* ]] && [[ $# > 1 ]]; do
@@ -79,7 +81,7 @@ for fmri_niigz in ${fmri_list[@]}; do
     fmri_tag="sub-${sub}/${intended_tag}"
 
     cp "${fmri_niigz}" "${bids_dir}/${fmri_tag}.nii.gz"
-    update_json.py --jsonfile ${fmri_json} --polarity + \
+    update_json.py --fmri_niigz ${fmri_niigz} --polarity + --slicetiming "${slicetiming}" \
         > "${bids_dir}/${fmri_tag}.json"
 
     intended_tags=(${intended_tags[@]} "${intended_tag}.nii.gz")
@@ -94,13 +96,13 @@ if [ -n "${rpefwd_niigz}" ]; then
     rpefwd_json="${rpefwd_niigz%.nii.gz}.json"
     rpefwd_tag="sub-${sub}/ses-${ses}/fmap/sub-${sub}_ses-${ses}_dir-fwd_epi"
     cp "${rpefwd_niigz}" "${bids_dir}/${rpefwd_tag}.nii.gz"
-    update_json.py --jsonfile ${rpefwd_json} --polarity + --intendedfor ${intended_tags[@]} \
+    update_json.py --fmri_niigz ${rpefwd_niigz} --polarity + --intendedfor ${intended_tags[@]} \
         > "${bids_dir}/${rpefwd_tag}.json"
 
     rperev_json="${rperev_niigz%.nii.gz}.json"
     rperev_tag="sub-${sub}/ses-${ses}/fmap/sub-${sub}_ses-${ses}_dir-rev_epi"
     cp "${rperev_niigz}" "${bids_dir}/${rperev_tag}.nii.gz"
-    update_json.py --jsonfile ${rperev_json} --polarity - --intendedfor ${intended_tags[@]} \
+    update_json.py --fmri_niigz ${rperev_niigz} --polarity - --intendedfor ${intended_tags[@]} \
         > "${bids_dir}/${rperev_tag}.json"
 
 fi

diff --git a/src/update_json.py b/src/update_json.py
@@ -2,32 +2,71 @@
 
 import argparse
 import json
+import nibabel
 import sys
 
 parser = argparse.ArgumentParser()
-parser.add_argument('--jsonfile')
+parser.add_argument('--fmri_niigz')
 parser.add_argument('--polarity')
 parser.add_argument('--intendedfor', nargs='*')
+parser.add_argument('--slicetiming')
 args = parser.parse_args()
 
-with open(args.jsonfile) as f:
+
+jsonfile = args.fmri_niigz.replace('.nii.gz','.json')
+with open(jsonfile) as f:
     jobj = json.loads(f.read())
-
-    # Verify that this is a Philips scan before applying the Philips-
-    # specific fixes for TotalReadoutTime and PhaseEncodingDirection
-    if jobj['Manufacturer'] != 'Philips':
-        raise Exception(f'Manufacturer is {jobj["Manufacturer"]} - expecting Philips')
-
-    jobj['TotalReadoutTime'] = jobj['EstimatedTotalReadoutTime']
-
-    if args.polarity=='+':
-        jobj['PhaseEncodingDirection'] = jobj['PhaseEncodingAxis']
-    elif args.polarity=='-':
-        jobj['PhaseEncodingDirection'] = jobj['PhaseEncodingAxis'] + '-'
+
+
+## Phase encoding direction/info
+
+# Verify that this is a Philips scan before applying the Philips-
+# specific fixes for TotalReadoutTime and PhaseEncodingDirection
+if jobj['Manufacturer'] != 'Philips':
+    raise Exception(f'Manufacturer is {jobj["Manufacturer"]} - expecting Philips')
+
+jobj['TotalReadoutTime'] = jobj['EstimatedTotalReadoutTime']
+
+if args.polarity=='+':
+    jobj['PhaseEncodingDirection'] = jobj['PhaseEncodingAxis']
+elif args.polarity=='-':
+    jobj['PhaseEncodingDirection'] = jobj['PhaseEncodingAxis'] + '-'
+else:
+    raise Exception(f'Unknown polarity {args.polarity}')
+
+if args.intendedfor:
+    jobj['IntendedFor'] = args.intendedfor
+
+
+## Slice timing
+
+if args.slicetiming:
+
+    # Get number of slices and TR from .nii.gz. Assume
+    # slice axis is the third one.
+    nii = nibabel.load(args.fmri_niigz)
+    nslices = nii.header['dim'][3]
+    tr = nii.header['pixdim'][4]
+
+    # Check for existing
+    if 'SliceTiming' in jobj:
+        raise Exception(f'SliceTiming field exists in {jsonfile}')
+    if 'SliceEncodingDirection' in jobj:
+        raise Exception(f'SliceEncodingDirection field exists in {jsonfile}')
+
+    # Get repetition time from .json to crosscheck
+    tr2 = jobj['RepetitionTime']
+    if abs(tr2-tr)>0.001:
+        raise Exception(f'TR in {jsonfile} does not match {args.fmri_niigz}')
+
+    # We can only handle certain specific cases
+    #    Philips_ASCEND_k: ascending on third axis
+    if args.slicetiming=='Philips_ASCEND_k':
+        jobj['SliceEncodingDirection'] = 'k'
+        jobj['SliceTiming'] = list(range(0,nslices) / nslices * tr)
     else:
-        raise Exception(f'Unknown polarity {args.polarity}')
+        raise Exception(f'Cannot handle slice timing of {args.slicetiming}')
+
 
-    if args.intendedfor:
-        jobj['IntendedFor'] = args.intendedfor
-
-    print(json.dumps(jobj, indent = 4))
+## Print it out
+print(json.dumps(jobj, indent = 4))