updating fit

Author: gonzoBlackMamba

rerun_pydesigner_fit_bids.sh

@@ -0,0 +1,229 @@
+#!/usr/bin/env bash
+
+set -euo pipefail
+
+# ============================================================
+# Batch rerun PyDesigner fitting-only script over BIDS subjects
+#
+# Expected layout from the original run_pydesigner_bids.sh:
+#   BIDS_ROOT/
+#     sub-*/dwi/*_dir-AP_dwi.nii.gz
+#     sub-*/dwi/*_dir-PA_dwi.nii.gz
+#     derivatives/dki/sub-*/dwi_preprocessed.nii[.gz]
+#     derivatives/dki/sub-*/dwi_preprocessed.bvec
+#     derivatives/dki/sub-*/dwi_preprocessed.bval
+#     derivatives/dki/sub-*/brain_mask.nii[.gz]
+#
+# The new run_pydesigner_fit.py is then called on each subject's
+# preprocessed PyDesigner files.
+# ============================================================
+
+# -----------------------------
+# User settings
+# -----------------------------
+
+# Run from the BIDS root, or pass BIDS root as first argument:
+#   ./rerun_pydesigner_fit_bids.sh /path/to/bids_root
+BIDS_ROOT="${1:-$(pwd)}"
+DERIV_ROOT="${DERIV_ROOT:-${BIDS_ROOT}/derivatives/dki}"
+
+# Path to your updated fitting-only Python script.
+# Edit this or export FIT_SCRIPT=/path/to/run_pydesigner_fit.py before running.
+FIT_SCRIPT="${FIT_SCRIPT:-${BIDS_ROOT}/run_pydesigner_fit.py}"
+PYTHON_CMD="${PYTHON_CMD:-python}"
+
+# New output subdirectory under each subject's derivatives/dki/sub-* folder.
+# Using a new folder avoids overwriting the original PyDesigner outputs.
+METRICS_DIR_NAME="${METRICS_DIR_NAME:-metrics_refit}"
+
+# Fit options for run_pydesigner_fit.py
+NTHREADS="${NTHREADS:-8}"
+RES="${RES:-med}"
+LMAX_FBI="${LMAX_FBI:-6}"
+BVEC_FLIP_X="${BVEC_FLIP_X:-1}"
+BVEC_FLIP_Y="${BVEC_FLIP_Y:--1}"
+BVEC_FLIP_Z="${BVEC_FLIP_Z:-1}"
+
+# Set these to 0 if you do not want them passed.
+DO_RECTIFY="${DO_RECTIFY:-1}"
+DO_FBWM="${DO_FBWM:-1}"
+
+# Set DRY_RUN=1 to print commands without executing.
+DRY_RUN="${DRY_RUN:-0}"
+
+# Set SKIP_IF_DONE=1 to skip subjects with existing key outputs.
+SKIP_IF_DONE="${SKIP_IF_DONE:-0}"
+
+# -----------------------------
+# Helpers
+# -----------------------------
+
+find_first() {
+    local root="$1"
+    shift
+
+    local pattern
+    local hit
+    for pattern in "$@"; do
+        hit="$(find "${root}" -type f -name "${pattern}" -print | head -n 1 || true)"
+        if [[ -n "${hit}" ]]; then
+            echo "${hit}"
+            return 0
+        fi
+    done
+
+    return 1
+}
+
+require_file() {
+    local label="$1"
+    local file="$2"
+    if [[ -z "${file}" || ! -f "${file}" ]]; then
+        echo "[MISSING] ${label}: ${file:-not found}"
+        return 1
+    fi
+    return 0
+}
+
+# -----------------------------
+# Checks
+# -----------------------------
+
+if [[ ! -d "${BIDS_ROOT}" ]]; then
+    echo "[ERROR] BIDS_ROOT does not exist: ${BIDS_ROOT}"
+    exit 1
+fi
+
+if [[ ! -d "${DERIV_ROOT}" ]]; then
+    echo "[ERROR] DERIV_ROOT does not exist: ${DERIV_ROOT}"
+    echo "        Did the original PyDesigner BIDS run finish?"
+    exit 1
+fi
+
+if [[ ! -f "${FIT_SCRIPT}" ]]; then
+    echo "[ERROR] FIT_SCRIPT does not exist: ${FIT_SCRIPT}"
+    echo "        Edit FIT_SCRIPT in this script or export FIT_SCRIPT=/path/to/run_pydesigner_fit.py"
+    exit 1
+fi
+
+RECTIFY_FLAG=()
+FBWM_FLAG=()
+if [[ "${DO_RECTIFY}" == "1" ]]; then
+    RECTIFY_FLAG=(--rectify)
+fi
+if [[ "${DO_FBWM}" == "1" ]]; then
+    FBWM_FLAG=(--fbwm)
+fi
+
+# -----------------------------
+# Main loop
+# -----------------------------
+
+for SUB_DIR in "${BIDS_ROOT}"/sub-*; do
+    if [[ ! -d "${SUB_DIR}" ]]; then
+        continue
+    fi
+
+    SUB_ID="$(basename "${SUB_DIR}")"
+    RAW_DWI_DIR="${SUB_DIR}/dwi"
+    PYD_DIR="${DERIV_ROOT}/${SUB_ID}"
+    OUT_DIR="${PYD_DIR}/${METRICS_DIR_NAME}"
+    LOG_DIR="${PYD_DIR}/logs"
+    LOG_FILE="${LOG_DIR}/fit_rerun_${SUB_ID}.log"
+
+    echo "============================================================"
+    echo "Subject: ${SUB_ID}"
+    echo "Raw DWI dir        : ${RAW_DWI_DIR}"
+    echo "PyDesigner deriv dir: ${PYD_DIR}"
+    echo "Refit output      : ${OUT_DIR}"
+    echo "============================================================"
+
+    if [[ ! -d "${RAW_DWI_DIR}" ]]; then
+        echo "[SKIP] Missing raw BIDS DWI directory: ${RAW_DWI_DIR}"
+        echo
+        continue
+    fi
+
+    if [[ ! -d "${PYD_DIR}" ]]; then
+        echo "[SKIP] Missing PyDesigner derivative directory: ${PYD_DIR}"
+        echo
+        continue
+    fi
+
+    DWI="$(find_first "${PYD_DIR}" "dwi_preprocessed.nii" "dwi_preprocessed.nii.gz" || true)"
+    BVEC="$(find_first "${PYD_DIR}" "dwi_preprocessed.bvec" || true)"
+    BVAL="$(find_first "${PYD_DIR}" "dwi_preprocessed.bval" || true)"
+    MASK="$(find_first "${PYD_DIR}" "brain_mask.nii" "brain_mask.nii.gz" || true)"
+
+    missing=0
+    require_file "preprocessed DWI" "${DWI}" || missing=1
+    require_file "preprocessed bvec" "${BVEC}" || missing=1
+    require_file "preprocessed bval" "${BVAL}" || missing=1
+    require_file "brain mask" "${MASK}" || missing=1
+    if [[ "${missing}" == "1" ]]; then
+        echo "[SKIP] Required fitting inputs not found for ${SUB_ID}"
+        echo
+        continue
+    fi
+
+    mkdir -p "${OUT_DIR}" "${LOG_DIR}"
+
+    if [[ "${SKIP_IF_DONE}" == "1" ]]; then
+        if [[ -f "${OUT_DIR}/dti_fa.nii" || -f "${OUT_DIR}/dki_mk.nii" || -f "${OUT_DIR}/fbi_faa.nii" ]]; then
+            echo "[SKIP] Existing refit outputs found in ${OUT_DIR}"
+            echo
+            continue
+        fi
+    fi
+
+    CMD=(
+        "${PYTHON_CMD}" "${FIT_SCRIPT}"
+        --dwi "${DWI}"
+        --bvec "${BVEC}"
+        --bval "${BVAL}"
+        --mask "${MASK}"
+        --out "${OUT_DIR}"
+        --nthreads "${NTHREADS}"
+        --res "${RES}"
+        --lmax-fbi "${LMAX_FBI}"
+        "${RECTIFY_FLAG[@]}"
+        "${FBWM_FLAG[@]}"
+        --bvec-flips "${BVEC_FLIP_X}" "${BVEC_FLIP_Y}" "${BVEC_FLIP_Z}"
+    )
+
+    echo "[RUN] Fitting-only PyDesigner rerun for ${SUB_ID}"
+    echo "[LOG] ${LOG_FILE}"
+    echo "Command:"
+    printf '  %q' "${CMD[@]}"
+    echo
+
+    if [[ "${DRY_RUN}" == "1" ]]; then
+        echo "[DRY RUN] Command not executed."
+        echo
+        continue
+    fi
+
+    {
+        echo "Started: $(date)"
+        echo "Subject: ${SUB_ID}"
+        echo "DWI : ${DWI}"
+        echo "BVEC: ${BVEC}"
+        echo "BVAL: ${BVAL}"
+        echo "MASK: ${MASK}"
+        echo "OUT : ${OUT_DIR}"
+        echo "Command:"
+        printf '  %q' "${CMD[@]}"
+        echo
+        echo
+
+        "${CMD[@]}"
+
+        echo
+        echo "Finished: $(date)"
+    } 2>&1 | tee "${LOG_FILE}"
+
+    echo "[DONE] ${SUB_ID}"
+    echo
+done
+
+echo "All available subjects processed."