Richard Nkrumah
9a5e36bae2
The code was written by Richard for q01-mannheim/q01-bids-dataset and shared in a discussion thread (all/status/issues/1). It is included here because I can't access the original repo.
92 lines
2.3 KiB
Bash
Executable file
92 lines
2.3 KiB
Bash
Executable file
#!/usr/bin/env bash
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set -euo pipefail
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BIDS_ROOT="${1:-.}"
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find "$BIDS_ROOT" -type d -path "*/sub-*/ses-*/dwi" | while read -r DWI_DIR; do
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SES_DIR="$(dirname "$DWI_DIR")"
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FMAP_DIR="${SES_DIR}/fmap"
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mkdir -p "$FMAP_DIR"
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for DWI_NII in "$DWI_DIR"/sub-*_ses-*_acq-b1200_dwi.nii.gz; do
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[ -e "$DWI_NII" ] || continue
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DWI_BASE="${DWI_NII%.nii.gz}"
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STEM="$(basename "$DWI_BASE" _dwi)"
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SUBSES="${STEM%_acq-b1200}"
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OLD_DWI="${DWI_DIR}/${STEM}_dwi"
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NEW_DWI="${DWI_DIR}/${STEM}_dir-PA_dwi"
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OLD_SBREF="${DWI_DIR}/${SUBSES}_acq-b1200_sbref"
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NEW_EPI="${FMAP_DIR}/${SUBSES}_acq-b1200_dir-AP_epi"
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echo "Processing ${SUBSES}"
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for ext in nii.gz json bval bvec; do
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if [ -e "${OLD_DWI}.${ext}" ] && [ ! -e "${NEW_DWI}.${ext}" ]; then
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git mv "${OLD_DWI}.${ext}" "${NEW_DWI}.${ext}"
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fi
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done
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for ext in nii.gz json; do
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if [ -e "${OLD_SBREF}.${ext}" ] && [ ! -e "${NEW_EPI}.${ext}" ]; then
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git mv "${OLD_SBREF}.${ext}" "${NEW_EPI}.${ext}"
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fi
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done
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for ext in bval bvec; do
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if [ -e "${OLD_SBREF}.${ext}" ]; then
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git rm "${OLD_SBREF}.${ext}"
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fi
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done
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EPI_JSON="${NEW_EPI}.json"
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DWI_REL="$(basename "$SES_DIR")/dwi/$(basename "${NEW_DWI}.nii.gz")"
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if [ -e "$EPI_JSON" ]; then
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datalad unlock "$EPI_JSON" || true
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python3 - <<PY
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import json
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from pathlib import Path
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p = Path("$EPI_JSON")
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with p.open("r", encoding="utf-8") as f:
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data = json.load(f)
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data["IntendedFor"] = ["$DWI_REL"]
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with p.open("w", encoding="utf-8") as f:
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json.dump(data, f, indent=2)
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f.write("\\n")
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PY
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fi
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SCANS_TSV="${SES_DIR}/$(basename "$(dirname "$SES_DIR")")_$(basename "$SES_DIR")_scans.tsv"
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if [ -e "$SCANS_TSV" ]; then
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datalad unlock "$SCANS_TSV" || true
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python3 - <<PY
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from pathlib import Path
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p = Path("$SCANS_TSV")
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txt = p.read_text()
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repls = {
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"dwi/$(basename "${OLD_DWI}.nii.gz")": "dwi/$(basename "${NEW_DWI}.nii.gz")",
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"dwi/$(basename "${OLD_DWI}.json")": "dwi/$(basename "${NEW_DWI}.json")",
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"dwi/$(basename "${OLD_SBREF}.nii.gz")": "fmap/$(basename "${NEW_EPI}.nii.gz")",
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"dwi/$(basename "${OLD_SBREF}.json")": "fmap/$(basename "${NEW_EPI}.json")",
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}
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for old, new in repls.items():
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txt = txt.replace(old, new)
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p.write_text(txt)
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PY
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fi
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done
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done
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datalad save -m "Fix DWI reverse PE fieldmap structure for QSIPrep SDC"
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