Upload bb_asl_visual_check

ASL_pipeline/bb_asl_visual_check.sh

+#!/bin/sh
+#
+# Script name: bb_asl_visual_check
+#
+# Description: Script to visually inspect the output of the ASL processing pipeline
+#
+# Authors: Thomas Okell, Flora Kennedy McConnell
+#
+# 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.
+#
+
+CURDIR=`pwd`
+echo Current directory\: $CURDIR
+
+cd PerfQuantFull/fsl* 
+echo Check motion...
+fsleyes asldata -dr 0 1500 asldata_orig -dr 0 1500
+
+echo Check distortion correction...
+fsleyes calib_orig.nii.gz calib_wholehead.nii.gz
+
+echo Check alignment with structural is better after distortion correction...
+fsleyes  ../../../T1/T1_unbiased \
+    calib_orig.nii.gz -a 50 -dr 900 3000 -cm blue-lightblue \
+    calib_wholehead.nii.gz -a 50 -dr 900 3000 -cm red-yellow  
+
+cd ../native_space
+echo Native space results...
+fsleyes aCBV_calib -dr 0 3 -cm brain_colours_6bluegrn \
+    arrival -dr 0.5 3.0 -cm hot \
+    pvcorr/perfusion_calib.nii.gz \
+    perfusion_calib -dr 0 100 \
+    ../fsl*/diffdata_mean.nii.gz -dr -10 50 
+    
+cd ../struct_space/
+echo Structural space results...
+fsleyes ../../../T1/T1_unbiased \
+    perfusion_calib.nii.gz -cm hot -dr 25 70 -a 50 \
+    ../../../T1/T1_fast/T1_brain_pve_1.nii.gz -dr 0.5 0.55 -cm green -a 50
+
+cd ../std_space
+echo Standard space results...
+fsleyes $FSLDIR/data/standard/MNI152_T1_2mm \
+    perfusion_calib.nii.gz -dr 25 70 -cm red-yellow -a 25
+
+cd $CURDIR
+echo DONE\!
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