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Merge pull request #21 from BIDS-Apps/fs
run recon_all if freesurfer directory not found and others
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.DS_Store | ||
.idea | ||
# Byte-compiled / optimized / DLL files | ||
__pycache__/ | ||
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#!/usr/bin/env bash | ||
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# cd /data.nfs/ds114/tracula_full_tests | ||
# screen -L bash run_full_tests_....sh ds114_test1 and | ||
# screen -L bash run_full_tests_....sh ds114_test2 | ||
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ds_name=$1 | ||
echo Running ${ds_name} | ||
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tracula_version=v6.0.0-3 | ||
wd=/data.nfs/ds114/tracula_full_tests/${tracula_version} | ||
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data_dir=${wd}/data | ||
out_root_dir=${wd}/out | ||
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mkdir -p $data_dir | ||
mkdir -p $out_root_dir | ||
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if [[ ! -d ${data_dir}/ds114_test1 ]]; then wget -c -O ${data_dir}/ds114_test1.tar "https://files.osf.io/v1/resources/9q7dv/providers/osfstorage/57e54a326c613b01d7d3ed90" && tar xf ${data_dir}/ds114_test1.tar -C ${data_dir}; fi | ||
if [[ ! -d ${data_dir}/ds114_test2 ]]; then wget -c -O ${data_dir}/ds114_test2.tar "https://files.osf.io/v1/resources/9q7dv/providers/osfstorage/57e549f9b83f6901d457d162" && tar xf ${data_dir}/ds114_test2.tar -C ${data_dir}; fi | ||
if [[ ! -d ${data_dir}/ds114_test1_freesurfer_precomp_v6.0.0 ]]; then wget -c -O ${data_dir}/ds114_test1_freesurfer.tar "https://osf.io/j6zk2/?action=download&version=1" && tar xf ${data_dir}/ds114_test1_freesurfer.tar -C ${data_dir}; fi | ||
if [[ ! -d ${data_dir}/ds114_test2_freesurfer_precomp_v6.0.0 ]]; then wget -c -O ${data_dir}/ds114_test2_freesurfer.tar "https://osf.io/yhzzj/?action=download&version=1" && tar xf ${data_dir}/ds114_test2_freesurfer.tar -C ${data_dir}; fi | ||
if [[ -e ${data_dir}/*.tar ]]; then rm -r ${data_dir}/*.tar; fi | ||
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in_dir=${data_dir}/${ds_name} | ||
fs_dir=${data_dir}/${ds_name}_freesurfer_precomp_v6.0.0 | ||
out_dir=${out_root_dir}/${ds_name} | ||
mkdir -p $out_dir | ||
chmod -R 777 $out_dir | ||
cd $out_dir | ||
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docker run --rm -ti \ | ||
-v ${in_dir}:/data/in \ | ||
-v ${fs_dir}:/data/fs \ | ||
-v ${out_dir}:/data/out \ | ||
bids/tracula:${tracula_version} \ | ||
/data/in /data/out participant \ | ||
--license_key xxx \ | ||
--freesurfer_dir /data/fs | ||
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docker run --rm -ti \ | ||
-v ${in_dir}:/data/in \ | ||
-v ${fs_dir}:/data/fs \ | ||
-v ${out_dir}:/data/out \ | ||
bids/tracula:${tracula_version} \ | ||
/data/in /data/out group1 \ | ||
--license_key xxx \ | ||
--freesurfer_dir /data/fs | ||
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docker run --rm -ti \ | ||
-v ${in_dir}:/data/in \ | ||
-v ${fs_dir}:/data/fs \ | ||
-v ${out_dir}:/data/out \ | ||
bids/tracula:${tracula_version} \ | ||
/data/in /data/out group2 \ | ||
--license_key xxx \ | ||
--freesurfer_dir /data/fs | ||
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tar -zcvf ${wd}/results_tracula_${tracula_version}_${ds_name}.tar.gz ${out_dir} | ||
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