example_run_maTT.sh

#!/bin/bash

# did you checkout the maTT2 example? because it does the same thing
# as maTT, but much faster. At this point, I'd really only recommend
# this old maTT version for people who _really_ know what they are 
# doing and have decided this is the functionality they want...

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# SETUP FSL HERE (however it is done on your system)
# export FSLDIR=/programs/fsl/
# source ${FSLDIR}/etc/fslconf/fsl.sh

# SETUP FREESUFER HERE (however it is done on your system)
# module load freesurfer/5.3.0

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# export variables to maTT_main.sh

export atlasBaseDir=${PWD}/atlas_data/
export scriptBaseDir=${PWD}/
# make a list from these options: 
# nspn500 gordon333 yeo17dil hcp-mmp-b schaefer100-yeo17 
# schaefer200-yeo17 schaefer400-yeo17 schaefer600-yeo17 schaefer800-yeo17 
export atlasList="schaefer100-yeo17 schaefer200-yeo17 yeo17"

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# subject variables

subj="my_subject"
inputFSDir="/path/to/freesurfer/${subj}/"
outputDir="/output/to/somwhere/${subj}/"
mkdir -p ${outputDir}

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# go into the folder where we also want output and setup notes file!

cd ${outputDir}
OUT="maTT_notes.txt"
touch $OUT

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# run the script

# script inputs:
# -d inputFSDir --> input freesurfer directory
# -o outputDir ---> output directory, will also write temporary 
#                   files here 
# optional inputs:
# -r refBrain ----> file to be used as reference when transfering 
#                   aparc+aseg.mgz to orginal (native) space.
# -n numThread ---> number of parallel processes to use when doing
#                   the label transfer

start=`date +%s`

cmd="${scriptBaseDir}/src/maTT_main.sh \
        -d ${inputFSDir} \
        -o ${outputDir} \
    "
echo $cmd 
eval $cmd | tee -a ${OUT}

# record how long that took!
end=`date +%s`
runtime=$((end-start))
echo "runtime: $runtime"