M2-PCASL-CBF/icc_map_roi.sh at master · Jody-Todd/M2-PCASL-CBF · GitHub

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#!/bin/bash

# This script computes the average ICC within ROIs: GM, WM, frontal lobe, parietal lobe, occipital lobe, and temporal lobe. ROIs defined by AAL atlas.
#
# Parameters:
#	$1: ICC map in MNI space

if [ $# -lt 1 ]; then echo "Input ICC map in MNI space."; exit; fi

export FSLOUTPUTTYPE=NIFTI

input_img=$1
filename=$(basename "$input_img")
filename=${filename%.nii}
dir=$(dirname $input_img)

fslmaths aal_MNI_V4.nii -thr 1 -uthr 28 -bin frontal_aal_mask.nii
fslmaths aal_MNI_V4.nii -thr 43 -uthr 56 -bin occipital_aal_mask.nii
fslmaths aal_MNI_V4.nii -thr 57 -uthr 70 -bin parietal_aal_mask.nii
fslmaths aal_MNI_V4.nii -thr 79 -uthr 90 -bin temporal_aal_mask.nii
fslmaths aal_MNI_V4.nii -thr 37 -uthr 40 -bin hippocampus_aal_mask.nii
fslmaths aal_MNI_V4.nii -thr 41 -uthr 42 -bin amygdala_aal_mask.nii

fslmaths $input_img -mas frontal_aal_mask.nii "${dir}/${filename}_frontal.nii"
fslmaths $input_img -mas occipital_aal_mask.nii "${dir}/${filename}_occipital.nii"
fslmaths $input_img -mas parietal_aal_mask.nii "${dir}/${filename}_parietal.nii"
fslmaths $input_img -mas temporal_aal_mask.nii "${dir}/${filename}_temporal.nii"
fslmaths $input_img -mas hippocampus_aal_mask.nii "${dir}/${filename}_hippocampus.nii"
fslmaths $input_img -mas amygdala_aal_mask.nii "${dir}/${filename}_amygdala.nii"

fslmaths $input_img -mas gm_MNI_mask.nii "${dir}/${filename}_gm.nii"
fslmaths $input_img -mas wm_MNI_mask.nii "${dir}/${filename}_wm.nii"


# get summary stats

echo "frontal mean and standard deviation: ";  fslstats "${dir}/${filename}_frontal.nii" -n -M -s
echo "occipital mean and standard deviation: ";  fslstats "${dir}/${filename}_occipital.nii" -n -M -s
echo "parietal mean and standard deviation: ";  fslstats "${dir}/${filename}_parietal.nii" -n -M -s
echo "temporal mean and standard deviation: ";  fslstats "${dir}/${filename}_temporal.nii" -n -M -s
echo "hippocampus mean and standard deviation: ";  fslstats "${dir}/${filename}_hippocampus.nii" -n -M -s
echo "amygdala mean and standard deviation: ";  fslstats "${dir}/${filename}_amygdala.nii" -n -M -s
echo "GM  mean and standard deviation: ";  fslstats "${dir}/${filename}_gm.nii" -n -M -s
echo "WM mean and standard deviation: ";  fslstats "${dir}/${filename}_wm.nii" -n -M -s
echo "whole brain mean and standard deviation: ";  fslstats "$input_img" -n -M -s