DBS-ElecNet/run_saline at main · BRAIN-TO/DBS-ElecNet · GitHub

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#!/usr/bin/env bash
set -euo pipefail

# ----------------------------
# Usage
# ----------------------------
if [[ $# -ne 2 ]]; then
    echo "Usage: $0 <nifti_file> <num_elec (1 or 2)>"
    exit 1
fi

nifti_file="$1"
num_elec="$2"

# ----------------------------
# Validate inputs
# ----------------------------
if [[ ! -f "$nifti_file" ]]; then
    echo "Error: file not found: $nifti_file"
    exit 1
fi

if [[ "$num_elec" != "1" && "$num_elec" != "2" ]]; then
    echo "Error: num_elec must be 1 or 2"
    exit 1
fi

base="${nifti_file%.nii*}"

# ----------------------------
# Get original size
# ----------------------------
orig_size=$(python3 utils/get_size.py --input "$nifti_file")
echo "Original size: $orig_size"

# ----------------------------
# Preprocessing
# ----------------------------
echo "Resampling to 1mm isotropic..."
ResampleImage 3 "$nifti_file" "${base}_1mm_iso.nii.gz" 1.0x1.0x1.0 0 3['l']

echo "Running SynthStrip..."
mri_synthstrip \
    -i "${base}_1mm_iso.nii.gz" \
    -m "${base}_1mm_iso_brain_mask.nii.gz" \
    -o "${base}_1mm_iso_skull_striped.nii.gz"

echo "N4 bias correction..."
N4BiasFieldCorrection -d 3 \
    -x "${base}_1mm_iso_brain_mask.nii.gz" \
    -i "${base}_1mm_iso_skull_striped.nii.gz" \
    -o "${base}_1mm_iso_skull_striped_n4.nii.gz"

echo "Running SynthSeg..."
mri_synthseg \
    --i "${base}_1mm_iso_skull_striped_n4.nii.gz" \
    --o "${base}_1mm_iso_skull_striped_n4_seg.nii.gz" \
    --threads 5

# ----------------------------
# Run SALINE
# ----------------------------
if [[ "$num_elec" -eq 2 ]]; then
    echo "Running SALINE (dual electrode)..."
    python3 SALINE/elec_seg.py \
        --input "${base}_1mm_iso_skull_striped_n4.nii.gz" \
        --br_mask "${base}_1mm_iso_brain_mask.nii.gz" \
        --synthseg "${base}_1mm_iso_skull_striped_n4_seg.nii.gz"
else
    echo "Running SALINE (single electrode)..."
    python3 SALINE/elec_seg_single.py \
        --input "${base}_1mm_iso_skull_striped_n4.nii.gz" \
        --br_mask "${base}_1mm_iso_brain_mask.nii.gz" \
        --synthseg "${base}_1mm_iso_skull_striped_n4_seg.nii.gz"
fi

# ----------------------------
# Cleanup
# ----------------------------
echo "Cleaning intermediate files..."
rm -f \
    "${base}_1mm_iso_skull_striped.nii.gz" \
    "${base}_1mm_iso_brain_mask.nii.gz" \
    "${base}_1mm_iso_skull_striped_n4.nii.gz" \
    "${base}_1mm_iso_skull_striped_n4_seg.nii.gz"

# ----------------------------
# Resample back to native size
# ----------------------------
echo "Resampling result back to native space..."
ResampleImage 3 \
    "${base}_1mm_iso_saline_elec.nii.gz" \
    "${base}_saline_elec.nii.gz" \
    "$orig_size" 1 1

echo "Done."