Upload bb_tbss_md_NAWM

bb_tbss_md_NAWM

+#!/bin/bash
+#
+# Script name: bb_tbss_md_NAWM
+#
+# Description: Script to calculate MD values from WM tracts excluding WMH, i.e. normal appearing white matter (NAWM)
+#  (adapted pipeline from dMRI sequence with 3 diffusion directions)
+#
+# Authors: Ludovica Griffanti, Fidel Alfaro-Almagro, Stephen M. Smith & Mark Jenkinson
+#
+# 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.
+#
+
+. "$BB_BIN_DIR"/bb_pipeline_tools/bb_set_header 
+
+direc="$PWD"/"$1"
+TBSSDir="$direc"/dMRI/TBSS
+biancaDIR="$direc"/T2_FLAIR/lesions/
+
+################# Apply FNRIT warp to WMH to have WMH_to_MNI.nii.gz
+cd "$biancaDIR"
+
+$FSLDIR/bin/applywarp -i final_mask.nii.gz -o final_mask_to_MNI.nii.gz -r ${FSLDIR}/data/standard/MNI152_T1_1mm.nii.gz -w ../../T1/transforms/T1_to_MNI_warp.nii.gz
+
+################# Calculating IDPs masking out WMH
+cd "$TBSSDir"
+cd stats
+
+fslmaths ${biancaDIR}/final_mask_to_MNI.nii.gz -thr 0.2 -binv -mul all_MD all_MD_NAWM
+fslmaths all_MD_NAWM -mas mean_FA_skeleton_mask all_MD_NAWM_skeletonised
+fslstats -K ${FSLDIR}/data/atlases/JHU/JHU-ICBM-labels-1mm all_MD_NAWM_skeletonised.nii.gz -M >JHUrois_MD_NAWM.txt 
+
+cd ../..
+################# Saving IDPs in the main IDPs directory
+
+#Setting the string of NaN in case there is a problem.
+numVars="48"
+nanResult="";
+for i in $(seq 1 $numVars) ; do 
+    nanResult="NaN $nanResult" ; 
+done
+
+result="" 
+
+#for i in FA MD ; do
+for i in MD_NAWM ; do
+    if [ -f ${TBSSDir}/stats/JHUrois_${i}.txt ] ; then
+        if [ `cat ${TBSSDir}/stats/JHUrois_${i}.txt | wc -w` = $numVars ] ; then
+            miniResult=`cat ${TBSSDir}/stats/JHUrois_${i}.txt`
+        else
+            miniResult="$nanResult"
+        fi
+    else
+        miniResult="$nanResult"
+    fi
+    result="$result $miniResult"
+done
+
+echo $result > ${direc}/IDP_files/bb_IDP_diff_TBSS_NAWM.txt
+done
+
+. "$BB_BIN_DIR"/bb_pipeline_tools/bb_set_footer 
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