DTI/DTI_preprocessing_UNIX at main · erdemtaskiran/DTI · GitHub

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SUBJECTS_DIR="path to your subjects directory"
OUTPUT_DIR="      path to your output directory"

mkdir -p "$OUTPUT_DIR"

for subj in "$SUBJECTS_DIR"/SUB_*; do
    subj_name=$(basename "$subj")
    echo "Processing $subj_name..."

    DWI="$subj/${subj_name}.nii.gz"
    BVEC="$subj/${subj_name}.bvec"
    BVAL="$subj/${subj_name}.bval"
    REV="$subj/${subj_name}_rev.nii.gz"

    fslroi "$DWI" "$subj/${subj_name}_b0.nii.gz" 0 1
    fslroi "$REV" "$subj/${subj_name}_rev_b0.nii.gz" 0 1

    fslmerge -t "$subj/${subj_name}_b0_all.nii.gz" \
             "$subj/${subj_name}_rev_b0.nii.gz" \
             "$subj/${subj_name}_b0.nii.gz"

    topup --imain="$subj/${subj_name}_b0_all.nii.gz" \
          --datain="$SUBJECTS_DIR/acqparams.txt" \
          --config=b02b0.cnf \
          --out="$subj/${subj_name}_topup" \
          --iout="$subj/${subj_name}_topup_corrected_b0.nii.gz"

    bet "$subj/${subj_name}_topup_corrected_b0.nii.gz" \
        "$subj/${subj_name}_b0_brain.nii.gz" -f 0.25 -g 0 -m

    eddy --imain="$DWI" \
         --mask="$subj/${subj_name}_b0_brain_mask.nii.gz" \
         --acqp="$SUBJECTS_DIR/acqparams.txt" \
         --index="$SUBJECTS_DIR/index.txt" \
         --bvecs="$BVEC" \
         --bvals="$BVAL" \
         --topup="$subj/${subj_name}_topup" \
         --out="$subj/${subj_name}_eddy"

    dtifit --data="$subj/${subj_name}_eddy.nii.gz" \
           --mask="$subj/${subj_name}_b0_brain_mask.nii.gz" \
           --bvecs="$subj/${subj_name}_eddy.eddy_rotated_bvecs" \
           --bvals="$BVAL" \
           --out="$subj/${subj_name}_dti"

    flirt -in "$subj/${subj_name}_dti_FA.nii.gz" \
          -ref "$FSLDIR/data/standard/FMRIB58_FA_1mm" \
          -omat "$subj/${subj_name}_affine.mat" \
          -out "$subj/${subj_name}_FA_flirt.nii.gz"

    fnirt --in="$subj/${subj_name}_dti_FA.nii.gz" \
          --aff="$subj/${subj_name}_affine.mat" \
          --ref="$FSLDIR/data/standard/FMRIB58_FA_1mm" \
          --cout="$subj/${subj_name}_warp" \
          --iout="$subj/${subj_name}_FA_MNI.nii.gz"

    fslmaths "$subj/${subj_name}_FA_MNI.nii.gz" \
             -s 3.4 "$subj/${subj_name}_FA_MNI_smoothed.nii.gz"

    cp "$subj/${subj_name}_FA_MNI_smoothed.nii.gz" \
       "$OUTPUT_DIR/${subj_name}_FA_final.nii.gz"

    echo "Finished $subj_name"
    echo "-------------------------------"
done

echo "All subjects processed successfully."