make roi script

#!/bin/sh

# this is MERGED script for (i)transformation, (ii) roi making, and (iii) exclusion masking.

# THIS IS VERSION 2: FOR APARC+ASEGS2009S.

# THIS SCRIPT IS TO BE FOLLOWED BY TRAC_02_MAKEROILIST

cmd=$hr/batchcode/commands_roimerge

echo command file is $cmd

export FSLDIR=$WORK/fsl/fsl

for s in `cat $hr/fs/goodsubject.txt`

 do

cat <<EOM > $cmd

#!/bin/bash

#$ -l mem=3G,time=6::

#$ -cwd

#$ -V 

#$ -N roi

#$ -j y

#$ -o batchcode/roi

echo "Starting on : $(date)"

echo "Running on node : $(hostname)"

echo "Current directory : $(pwd)"

echo "Current job ID : $JOB_ID"

echo "Current job name : $JOB_NAME"

cd $hr/fs/$s/mri

echo -------------NOW MNI152REG WITH 1MM

export SUBJECTS_DIR=$hr/fs

mni152reg --s $s --1

echo -------------NOW CONVERTING MNI152.ORIG TO NII.GZ

mri_convert mni152.orig.mgz mni152.orig.nii.gz

fslreorient2std mni152.orig.nii.gz mni152.orig.orient.nii.gz

mri_convert orig.mgz orig.nii.gz

fslreorient2std orig.nii.gz orig.orient.nii.gz

echo -------------NOW TRANSFORMATION_REGISTRATION TO MNI152 TO CREATE FREESURFER2MAT.MAT

flirt -in orig.orient.nii.gz -ref mni152.orig.orient.nii.gz -omat ./transforms/freesurfer2mni152.mat -out ~/tmp

echo  -------------NOW TRANSFORMATION_REGISTRATION TO APARC+ASEG to MNI152 space USING FREESURFER2MAT.MAT

for im in aparc+aseg aparc.a2009s+aseg wmparc

do

        echo MRI_converting

mri_convert \${im}.mgz \${im}.nii.gz && fslreorient2std \${im}.nii.gz \${im}_orient.nii.gz

        echo FLIRTING1

        flirt -in \${im}_orient.nii.gz -ref mni152.orig.orient.nii.gz -applyxfm -init ./transforms/freesurfer2mni152.mat -interp nearestneighbour -omat ~/tmp -out \${im}_orient_mni152

echo FLIRTING2

        flirt -in \${im}_orient_mni152 -ref mni152.orig.orient.nii.gz -applyisoxfm 1 -out \${im}_orient_mni152_1mm

done

mv roi roi3 && mkdir roi

echo ------------NOW MAKING ALL ROI MASKS

#export roilist=$hr/fs/$s/mri/roi/roilist_wb.txt && rm \${roilist}

        

for roi in \`cat $WORK/code/roi_2009\` ;

do

echo MAKING ROI FOR \${roi}

fslmaths aparc.a2009s+aseg_orient_mni152_1mm -thr \${roi} -uthr \${roi} -bin ./roi/\${roi} && fslmaths ./roi/\${roi} -dilM ./roi/\${roi}_dil

# echo $hr/fs/$s/mri/roi/\${roi}_dil.nii.gz >> \${roilist}

done

#echo ------------NOW MAKING HIPPO-SUBDIVISION ROI MASKS (NIFTI CONVERSION, REORIENTATION, AND REGRSTATION)

#for lr in left right ;

#do 

#        for roi in CA1 CA2_3 CA4_DG fimbria hippocampal_fissure presubiculum subiculum ;

#        do

#        im=posterior_\${lr}_\${roi}

#        echo MAKING HIPPO-SUBDIVISION ROI FOR \$im

#        mri_convert \${im}.mgz \${im}.nii.gz && fslreorient2std \${im}.nii.gz \${im}_orient.nii.gz

#        echo FLIRTING-1

#        flirt -in \${im}_orient.nii.gz -ref mni152.orig.orient.nii.gz -applyxfm -init ./transforms/freesurfer2mni152.mat -interp nearestneighbour -out \${im}_orient_mni152

        

#        echo flirting-2

#        flirt -in \${im}_orient_mni152 -ref mni152.orig.orient.nii.gz -applyisoxfm 1 -out \${im}_orient_mni152_1mm

#         

# done

#done

echo -----------NOW EXCLUSION MASK

for roi in 4 43 14 15 72 24

do

echo MAKING EXCLUSION MASK \${roi}

fslmaths aparc+aseg_orient_mni152_1mm -thr \${roi} -uthr \${roi} -bin ./roi/\${roi} && fslmaths ./roi/\${roi} -dilM -bin ./roi/\${roi}_dil

done

echo -----------NOW EXCLUSION MASK from APARC_ASEG MASK

fslmaths aparc+aseg_orient_mni152_1mm -bin -mul -1 -add 1 ./roi/exclusionmask_additional

fslmaths ./roi/4 -add ./roi/43 -add ./roi/14 -add ./roi/15 -add ./roi/72 -add ./roi/24 -bin ./roi/exclusionmask

fslmaths ./roi/exclusionmask -add ./roi/exclusionmask_additional -bin ./roi/exclusionmask2  

echo ALL THE PREPRCESSING STEPS SUCCESSFULLY COMPLETED!!

EOM

#chmod +x $cmd

#cat $cmd

#ls $cmd

qsub $cmd

done