betpremask

mri_toolbox是一个工具用来MRI. 来自于SourceForge, 我上传这个软件,希望能结识对医疗软件感兴趣的兄弟.

#!/bin/sh

Usage() {
    echo "Usage: betpremask <inroot> <outroot> [-d]"
    echo "-d : don't delete intermediate files"
    exit
}

[ "$1" = "" ] && Usage

if [ _$FSLDIR = _ ] ; then
    FSLDIR=/usr/local/fsl
    export FSLDIR
fi

debug=0
if [ "$3" == "-d" ] ; then
  debug=1
fi

${FSLDIR}/bin/flirt -ref ${FSLDIR}/etc/standard/avg152T1 -in $1 -omat ${2}_tmp.mat -searchrx -180 180 -searchry -180 180 -searchrz -180 180
${FSLDIR}/bin/convert_xfm -omat ${2}_tmp_inv.mat -ref ${FSLDIR}/etc/standard/avg152T1 -in $1 -inverse ${2}_tmp.mat
${FSLDIR}/bin/flirt -ref $1 -in ${FSLDIR}/etc/standard/avg152T1_brain_mask_dil2 -out ${2}_tmp_mask -applyxfm -init ${2}_tmp_inv.mat
${FSLDIR}/bin/avwmaths $1 -mul ${2}_tmp_mask $2

if [ $debug = 0 ] ; then
    /bin/rm -f ${2}_tmp*
fi