Upload bb_asl_summary_measures.sh

bb_ASL/bb_asl_summary_measures.sh

+#!/bin/sh
+#
+# Script name: bb_asl_summary_measures
+#
+# Description: Script to generate more robust GM/WM masks and extract summary measures from ASL data
+#
+# Authors: Thomas Okell, Flora Kennedy McConnell, Ludovica Griffanti, Fidel Alfaro-Almagro
+#
+# Copyright 2021 University of Oxford
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#    http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+#. $BB_BIN_DIR/bb_pipeline_tools/bb_set_header 
+
+origDir=`pwd`
+direc=$1
+
+cd $direc/ASL/PerfQuantFull/native_space
+
+# Generate the mask: threshold at 50% and mask by brain mask also. WM same but threshold 0.8
+$FSLDIR/bin/fslmaths pvgm_inasl.nii.gz -mul mask.nii.gz -thr 0.5 -bin gm_mask_0.5
+$FSLDIR/bin/fslmaths pvwm_inasl.nii.gz -mul mask.nii.gz -thr 0.8 -bin wm_mask_0.8
+
+# Generate summary CBF and arrival metrics
+MEANGMCBF=`fslstats perfusion_calib -k gm_mask_0.5.nii.gz -m`
+echo "Mean GM CBF\: $MEANGMCBF"
+echo "$MEANGMCBF" > ../../CBF_gm_mean.txt
+MEANGMATT=`fslstats arrival -k gm_mask_0.5.nii.gz -m`
+echo "Mean GM ATT\: $MEANGMATT"
+echo "$MEANGMATT" > ../../ATT_gm_mean.txt
+# WM
+MEANWMCBF=`fslstats perfusion_calib -k wm_mask_0.8.nii.gz -m`
+echo "Mean WM CBF\: $MEANWMCBF"
+echo "$MEANWMCBF" > ../../CBF_wm_mean.txt
+MEANWMATT=`fslstats arrival -k wm_mask_0.8.nii.gz -m`
+echo "Mean WM ATT\: $MEANWMATT"
+echo "$MEANWMATT" > ../../ATT_wm_mean.txt
+
+# Generate pvcorr summary CBF and arrival metrics
+cd pvcorr
+MEANGMCBFpvcorr=`fslstats perfusion_calib -k ../gm_mask_0.5.nii.gz -m`
+echo "Mean GM CBF PVCORR\: $MEANGMCBFpvcorr"
+echo "$MEANGMCBFpvcorr" > ../../../CBF_pvcorr_gm_mean.txt
+MEANGMATTpvcorr=`fslstats arrival -k ../gm_mask_0.5.nii.gz -m`
+echo "Mean GM ATT PVCORR \: $MEANGMATTpvcorr"
+echo "$MEANGMATTpvcorr" > ../../../ATT_pvcorr_gm_mean.txt
+# WM
+MEANWMCBFpvcorr=`fslstats perfusion_wm_calib -k ../wm_mask_0.8.nii.gz -m`
+echo "Mean WM CBF PVCORR\: $MEANWMCBFpvcorr"
+echo "$MEANWMCBFpvcorr" > ../../../CBF_pvcorr_wm_mean.txt
+MEANWMATTpvcorr=`fslstats arrival_wm -k ../wm_mask_0.8.nii.gz -m`
+echo "Mean WM ATT PVCORR \: $MEANWMATTpvcorr"
+echo "$MEANWMATTpvcorr" > ../../../ATT_pvcorr_wm_mean.txt
+
+cd $origDir
+
+#. $BB_BIN_DIR/bb_pipeline_tools/bb_set_footer 
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