Upload segIntensity

OB_pipeline/cmore_segIntensity.sh

+#!/usr/bin/sh
+
+# Description: Script to generate T2-FLAIR intensity values (raw and normalised for WM) from Olfactory Bulbs segmentation
+# Author: Ludovica Griffanti
+#
+# 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.
+#
+
+#main analysis directory containing subjects dirs
+direc=$1
+subjectslist="/path/to/subj/list/subj.txt"
+outpath="/path/to/volume/measurement-output/"
+
+for sub in `cat ${subjectslist}`; do
+echo $sub
+cd ${direc}/${sub}/T2_FLAIR
+# assuming OB labels in subjects space are in ${sub}/T2_FLAIR dir and called ${sub}_ob_labels_trilinear.nii.gz
+
+fslmaths ${sub}_ob_labels_trilinear.nii.gz -mul T2_FLAIR_unbiased.nii.gz ${sub}_FLAIR_mul_ob_trilinear.nii.gz
+OBval=`fslstats ${sub}_FLAIR_mul_ob_trilinear.nii.gz -M`
+
+# WM mask created duriing main UKB pipeline:
+# https://git.fmrib.ox.ac.uk/falmagro/UK_biobank_pipeline_v_1/-/blob/master/bb_structural_pipeline/bb_struct_init
+# $FSLDIR/bin/fslmaths T1_fast/T1_brain_pve_2.nii.gz -thr 0.5 -bin T1_fast/T1_brain_WM_mask.nii.gz
+
+WMval=`fslstats T2_FLAIR_unbiased.nii.gz -k ${direc}/${sub}/T1/T1_fast/T1_brain_WM_mask.nii.gz -P 50`
+
+#saving intensity, reference value and normalised reference
+norm_OBval=`echo "scale=5; $OBval / $WMval" | bc -l`
+echo $sub $OBval $WMval $norm_OBval >> ${outpath}/OB_FLAIR_values.txt
+done
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