#!/bin/bash

# =============================================================================
# XCP-D Post-processing Pipeline — waves_3_6 TEST (single subject)
# Subject:   sub-110087
# Strategy:  aCompCor + motion regression
#            High-pass via cosine regressors (Steven/XCP-D developer rec.)
#            Interpolation + scrubbing (FD > 0.5mm) + smoothing (6mm FWHM)
# Sessions:  ses-ams03 (200 vols) + ses-lei06 (310 vols)
# No explicit bandpass filter — cosine regressors handle high-pass internally
# No parcellation — voxelwise NIfTI output for MATLAB tbCAPs
# XCP-D version: 0.14.1
# =============================================================================

# ── Paths ────────────────────────────────────────────────────────────────────
FMRIPREP_DIR="/data/jagavirialopez/NESDA/BIDS/BIDS_derivatives/waves_3_6"
OUTPUT_DIR="/data/jagavirialopez/NESDA/BIDS/BIDS_derivatives/waves_3_6_xcpd_test"
WORK_DIR="/data/jagavirialopez/NESDA/BIDS/work_xcpd_waves_3_6_test"
XCP_D_IMG="/data/jagavirialopez/xcp_d_0.14.1.sif"
FS_LICENSE="/data/jagavirialopez/freesurfer/license.txt"

# ── Test subject ─────────────────────────���───────────────────────────────────
TEST_SUBJECT="110087"

# ── Parameters ───────────────────────────────────────────────────────────────
NPROCS=15
OMP_NTHREADS=8
MEM_MB=105000        # in MB (105 GB)
FD_THRESH=0.5        # Scrubbing threshold in mm (Power et al. 2014)
SMOOTHING=6          # FWHM in mm
# NO explicit high-pass — cosine regressors handle this within GLM (XCP-D dev recommendation)

# ── Setup ────────────────────────────────────────────────────────────────────
mkdir -p ${OUTPUT_DIR} ${WORK_DIR}

echo "=========================================="
echo "XCP-D TEST RUN — single subject"
echo "Subject:           sub-${TEST_SUBJECT}"
echo "Mode:              none (custom settings)"
echo "Confound strategy: aCompCor + cosine regressors (high-pass)"
echo "FD threshold:      ${FD_THRESH} mm"
echo "Smoothing:         ${SMOOTHING} mm FWHM"
echo "High-pass:         via cosine regressors (no explicit bandpass)"
echo "Low-pass:          none"
echo "Threads:           ${NPROCS}"
echo "Memory:            ${MEM_MB} MB"
echo "Output dir:        ${OUTPUT_DIR}"
echo "Started at:        $(date '+%Y-%m-%d %H:%M:%S')"
echo "=========================================="

singularity run --cleanenv \
    -B ${FMRIPREP_DIR}:${FMRIPREP_DIR} \
    -B ${OUTPUT_DIR}:${OUTPUT_DIR} \
    -B ${WORK_DIR}:${WORK_DIR} \
    -B $(dirname ${FS_LICENSE}):$(dirname ${FS_LICENSE}) \
    ${XCP_D_IMG} \
    ${FMRIPREP_DIR} \
    ${OUTPUT_DIR} \
    participant \
    --mode none \
    --participant-label ${TEST_SUBJECT} \
    --input-type fmriprep \
    --file-format nifti \
    --skip-parcellation \
    -p acompcor \
    --smoothing ${SMOOTHING} \
    -f ${FD_THRESH} \
    --disable-bandpass-filter \
    --output-type censored \
    --head-radius auto \
    --motion-filter-type none \
    --despike y \
    --combine-runs n \
    --warp-surfaces-native2std n \
    --linc-qc n \
    --abcc-qc n \
    --output-run-wise-correlations n \
    --min-coverage 0.5 \
    --fs-license-file ${FS_LICENSE} \
    --nprocs ${NPROCS} \
    --omp-nthreads ${OMP_NTHREADS} \
    --mem-mb ${MEM_MB} \
    --work-dir ${WORK_DIR} \
    --notrack \
    -v

exit_code=$?

echo ""
echo "=========================================="
echo "Finished at: $(date '+%Y-%m-%d %H:%M:%S')"

if [ ${exit_code} -ne 0 ]; then
    echo "STATUS: ❌ FAILED (exit code ${exit_code})"
    echo ""
    echo "Troubleshooting tips:"
    echo "  1. Check logs in: ${OUTPUT_DIR}/logs/"
    echo "  2. Check work dir: ${WORK_DIR}"
    echo "  3. Run with --stop-on-first-crash for detailed traceback"
else
    echo "STATUS: ✅ SUCCESS"
    echo ""
    echo "Expected outputs:"
    echo "  ${OUTPUT_DIR}/sub-${TEST_SUBJECT}/ses-ams03/func/"
    echo "  └── sub-${TEST_SUBJECT}_ses-ams03_task-rest_space-MNI152NLin6Asym_res-2_desc-denoised_bold.nii.gz"
    echo "  ${OUTPUT_DIR}/sub-${TEST_SUBJECT}/ses-lei06/func/"
    echo "  └── sub-${TEST_SUBJECT}_ses-lei06_task-rest_space-MNI152NLin6Asym_res-2_desc-denoised_bold.nii.gz"
    echo ""
    echo "QC report:"
    echo "  ${OUTPUT_DIR}/sub-${TEST_SUBJECT}.html"
fi

echo "=========================================="