Delete bb_tbss_md_NAWM.sh

bb_tbss_md_NAWM.sh

-#!/bin/bash
-
-. "$BB_BIN_DIR"/bb_pipeline_tools/bb_set_header 
-
-direc="$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 
\ No newline at end of file