mribrew_dwi_tbss.sh

#!/bin/bash

# Set FSL environment
. ${FSLDIR}/etc/fslconf/fsl.sh

# Directory structure
BASE_DIR="data/proc/dwi_proc"
OUTDIR="data/res/tbss"
mkdir -p ${OUTDIR}

# Find all subject directories
for subject_dir in ${BASE_DIR}/*/; do
    subject=$(basename ${subject_dir})
    date_dir=$(ls -d ${subject_dir}/*/ | head -n 1)
    
    # Define input paths for each subject
    DWI_PATH="${date_dir}/dwi/eddy_corrected.nii.gz"
    MASK_PATH="${date_dir}/dwi/dwi_mask.nii.gz"
    BVEC_PATH="${date_dir}/dwi/gradChecked.bvecs"
    BVAL_PATH="${date_dir}/dwi/gradChecked.bvals"
    
    # Check if all required files exist
    if [ ! -f ${DWI_PATH} ] || [ ! -f ${MASK_PATH} ] || [ ! -f ${BVEC_PATH} ] || [ ! -f ${BVAL_PATH} ]; then
        echo "Warning: Missing required files for subject ${subject}"
        continue
    fi
    
    # Fit diffusion tensor
    echo "Processing subject: ${subject}"
    dtifit --data=${DWI_PATH} \
           --mask=${MASK_PATH} \
           --bvecs=${BVEC_PATH} \
           --bvals=${BVAL_PATH} \
           --out=${OUTDIR}/${subject}
    
    # Remove all files except FA
    rm -f ${OUTDIR}/${subject}_L1.* \
          ${OUTDIR}/${subject}_L2.* \
          ${OUTDIR}/${subject}_L3.* \
          ${OUTDIR}/${subject}_MD.* \
          ${OUTDIR}/${subject}_MO.* \
          ${OUTDIR}/${subject}_S0.* \
          ${OUTDIR}/${subject}_V1.* \
          ${OUTDIR}/${subject}_V2.* \
          ${OUTDIR}/${subject}_V3.*
done

cd ${OUTDIR}

# ls -1 FA/*_FA.nii.gz

# Prepare FA images
echo "Running tbss_1_preproc..."
tbss_1_preproc *_FA.nii.gz

# Create FA target and skeleton
echo "Running tbss_2_reg..."
tbss_2_reg -T

# Project all FA images onto mean FA skeleton
echo "Running tbss_3_postreg..."
tbss_3_postreg -S

# Create mean FA mask and apply threshold
tbss_4_prestats 0.3

cd stats

# Run statistics (modify design.mat and design.con as needed)
randomise -i all_FA_skeletonised -o tbss \
          -m mean_FA_skeleton_mask \
          -d design.mat -t design.con \
          -n 5000 --T2

tbss_fill tbss_clustere_corrp_tstat1 0.25 \
      mean_FA tbss_clustere_corrp_tstat1_filled

echo "TBSS analysis completed!"