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+Bootstrap: docker
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+From: debian:buster-slim
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+
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+%setup
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+ mkdir -p ${SINGULARITY_ROOTFS}/batch
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+ mkdir -p ${SINGULARITY_ROOTFS}/code
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+ mkdir -p ${SINGULARITY_ROOTFS}/downloads
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+
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+ chmod -R 777 ${SINGULARITY_ROOTFS}/code
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+
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+%post
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+ apt-get update
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+ apt-get -y install wget unzip libxext6 libxt6 moreutils
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+
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+ # download software & unzip
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+ MCRURL="https://ssd.mathworks.com/supportfiles/downloads/R2017b/deployment_files/R2017b/installers/glnxa64/MCR_R2017b_glnxa64_installer.zip"
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+ # SPMURL="http://www.neuro.uni-jena.de/cat12/CAT12.8.1_r2042_R2017b_MCR_Linux.zip"
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+ SPMURL="http://141.35.69.218/cat12/CAT12.8.1_r2042_R2017b_MCR_Linux.zip"
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+
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+ cd /downloads
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+ wget "${MCRURL}" && unzip -d /downloads/MCR MCR_R2017b_glnxa64_installer.zip
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+ wget "${SPMURL}" && unzip -d /code/SPM CAT12.8.1_r2042_R2017b_MCR_Linux.zip
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+
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+
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+ # install MCR
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+ /downloads/MCR/install -mode silent -agreeToLicense yes
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+
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+ # generalize CAT12 version
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+ mv /code/SPM/CAT12.8.1_r2042_R2017b_MCR_Linux/ /code/SPM/MCR_Linux/
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+
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+ # install SPM
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+ /code/SPM/MCR_Linux/run_spm12.sh /usr/local/MATLAB/MATLAB_Runtime/v93 quit
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+ cd /code/SPM/MCR_Linux && chmod +rx run_spm12.sh spm12.sh spm12 spm12.ctf
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+
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+ # install CAT standalone interface
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+ STANDALONE="/code/SPM/MCR_Linux/standalone"
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+ cd ${STANDALONE} && chmod +rx *.sh
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+ cd /code && ln -s ${STANDALONE}/*.sh .
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+ cd /batch && ln -s ${STANDALONE}/*.m .
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+
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+ # set permissions
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+ find /code -type f -print0 | xargs -0 chmod +r
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+ find /code/SPM/MCR_Linux/spm12_mcr/ -name 'CAT.glnx86' -print0 | xargs -0 chmod +rx -R
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+ rm -f code/cat_standalone_segment_enigma.m
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+ wget https://raw.githubusercontent.com/juaml/CAT_stacking_container/refs/heads/bax24-patch-1/cat_standalone_segment_enigma.m?token=GHSAT0AAAAAACX63A3JYCV6T6VTYPTUXO5MZX2SXMQ -O /code/cat_standalone_segment_enigma.m
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+
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+ chmod -R 777 /code*
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+
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+ rm -fr /downloads
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+
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+ apt-get clean
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+ apt-get autoremove
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+
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+%environment
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+ export SPMROOT=/code/SPM/MCR_Linux
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+ export MCRROOT=/usr/local/MATLAB/MATLAB_Runtime/v93
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+ export MCR_INHIBIT_CTF_LOCK=1
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+
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+%runscript
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+ NOW=$(date +%s)
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+ exec /code/cat_standalone.sh "$@" 2>&1 |tee cat_$NOW.log
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+
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+%labels
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+ Authors Malgorzata Wierzba (m.wierzba@fz-juelich.de)
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+ Felix Hoffstaedter (f.hoffstaedter@fz-juelich.de)
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+ Version 1.1
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+
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+%help
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+
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+This container allows to run the standalone, compiled version of the
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+Computational Anatomy Toolbox (CAT), which is an extension to SPM
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+software. Using the container does not require the availability of a
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+MATLAB licence.
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+
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+The container includes:
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+
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+- MATLAB Compiler Runtime (R2017b, 9.3)
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+- Standalone version of SPM software (SPM12, r7771)
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+- Computational Anatomy Toolbox (CAT12.8 r2042)
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+- CAT interface scripts (cat_standalone.sh, cat_parallelize.sh).
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+
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+For more details on the exact version of the software used in this
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+container, please refer to the README file.
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+
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+
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+HOW TO USE:
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+
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+In principle this container allows you to perform the very same types
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+of analysis that are possible with the standalone version of CAT. It
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+is assumed that the user is familiar with the content of the batch
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+files dedicated for the use with the standalone version of CAT
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+(cat_standalone_segment.m, cat_standalone_simple.m,
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+cat_standalone_resample.m, cat_standalone_smooth.m) and can modify
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+their content according to his/her needs. For more details, please
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+refer to the CAT12 documentation and manual.
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+
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+
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+-- Available batch files --
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+
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+The content of the batch files can be explored by using the 'view' and
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+'copy' subcommands:
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+
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+singularity run <container> <subcommand> <batch file> <arguments>
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+
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+To view a batch file, use the 'view' subcommand:
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+
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+singularity run container.simg view cat_standalone_smooth.m
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+
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+To copy a batch file to your computer, use the 'copy' subcommand and
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+specify destination path as an additional argument:
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+
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+singularity run container.simg copy cat_standalone_smooth.m $HOME
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+
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+Make sure that the specified path is mounted to the container (more
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+information on this can be found below) and that you have write access
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+to this path!
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+
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+To copy all available batch files, use the 'all' argument:
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+
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+singularity run container.simg copy all $HOME
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+
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+
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+-- Running CAT --
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+
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+Run the CAT analysis with the following command:
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+singularity run --cleanenv <container> <batch file> <arguments>
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+
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+To use a default batch file, use one of the files included in the
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+container ('/batch'):
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+singularity run --cleanenv container.simg \
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+ -b /batch/cat_standalone_segment.m \
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+ T1.nii
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+
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+To use your own, customised batch file, simply specify its path:
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+singularity run --cleanenv container.simg \
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+ -b $HOME/cat_standalone_segment.m \
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+ T1.nii
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+
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+
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+-- Bind paths --
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+
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+Please note that most of the host files remain inaccessible from within
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+the container. By default the following directories are mounted within
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+the container: '$HOME', '/tmp', '/proc', '/sys', '/dev', and '$PWD'
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+(see the Singularity documentation for more details).
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+
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+If you want the container to be able to access other locations,
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+specify a bind path of your choice. For instance, to make the contents
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+of the '/data' folder on your computer available in the '/mnt' folder
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+inside the container, specify the mount point in the following way:
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+
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+singularity run --cleanenv --bind /data:/mnt container.simg \
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+ -b /batch/cat_standalone_segment.m \
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+ /mnt/T1.nii
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+
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+
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+EXAMPLES:
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+
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+USAGE:
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+ cat_standalone.sh filename(s) [-s spm_standalone_folder] [-m mcr_folder] [-b batch_file]
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+ [-a1 additional_argument1] [-a2 additional_argument2]
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+ [-a add_to_batch]
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+
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+ -s <DIR> | --spm <DIR> SPM12 folder of standalone version (can be also defined by SPMROOT)
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+ -m <DIR> | --mcr <DIR> Matlab Compiler Runtime (MCR) folder (can be also defined by MCRROOT)
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+ -b <FILE> | --batch <FILE> batch file to execute
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+ -a1 <STRING>| --arg1 <STRING> 1st additional argument (otherwise use defaults or batch)
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+ -a2 <STRING>| --arg2 <STRING> 2nd additional argument (otherwise use defaults or batch)
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+ -a <STRING> | --add <STRING> add option to batch file
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+
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+ The first occurance of the parameter "<UNDEFINED>" in the batch file will be replaced by the
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+ list of input files. You can use the existing batch files in this folder or create your own batch
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+ file with the SPM12 batch editor and leave the data field undefined. Please note that for creating
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+ your own batch file CAT12 has to be called in expert mode because the CAT12 standalone installation
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+ will only run in expert mode to allow more options.
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+ See cat_standalone_segment.m for an example.
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+
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+ You can also define one or two optional arguments to change other parameters that are indicated by
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+ "<UNDEFINED>" in the batch file. Please take care of the order of the "<UNDEFINED>" fields in the
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+ batch file! If no additional arguments are defined the default values are used.
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+ Also, you must use multiple quotes if the argument is a string (e.g. " 'your_string' ").
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+
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+ If you use a computer cluster it is recommended to use the batch files to only process one data set
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+ and use a job or queue tool to call the (single) jobs on the cluster.
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+
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+PURPOSE:
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+ Command line call of (CAT12) batch files for SPM12 standalone installation
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+
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+EXAMPLES
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+ -----------------------------------------------------------------------------------------------
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+ Segmentation
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+ -a1 TPM
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+ -a2 Shooting template
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+ -----------------------------------------------------------------------------------------------
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+ cat_standalone.sh -s $SPMROOT -m /Applications/MATLAB/MATLAB_Runtime/v93 \
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+ -b ${cwd}/cat_standalone_segment.m sTRIO0001.nii
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+ Preprocess (segment) the single file sTRIO0001.nii using the default CAT12 preprocessing batch.
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+ SPM12 standalone version is located in $SPMROOT and Matlab Compiler Runtime in
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+ /Applications/MATLAB/MATLAB_Runtime/v93.
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+
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+ cat_standalone.sh -s $SPMROOT -m /Applications/MATLAB/MATLAB_Runtime/v93 \
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+ -b ${cwd}/cat_standalone_segment.m sTRIO000*.nii.gz \
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+ -a1 " '${cat12_dir}/templates_MNI152NLin2009cAsym/TPM_Age11.5.nii' " \
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+ -a2 " '${cat12_dir}/templates_MNI152NLin2009cAsym/Template_0_GS1mm.nii' "
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+ Unzip and preprocess (segment) the files sTRIO0001.nii.gz using the default CAT12 preprocessing
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+ batch, but use the children TPM provided with CAT12 and a 1mm Shooting template (not provided
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+ with CAT12). Please note that zipped file can only be handled with this standalone batch and also
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+ note the multiple quotes for parameter a1 and a2.
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+
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+ cat_standalone.sh -s $SPMROOT -m /Applications/MATLAB/MATLAB_Runtime/v93 \
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+ -b ${cwd}/cat_standalone_segment.m sTRIO0001.nii \
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+ -a "matlabbatch{1}.spm.tools.cat.estwrite.output.surface = 0;"
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+ Preprocess (segment) the single file sTRIO0001.nii using the default CAT12 preprocessing batch,
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+ but skip surface estimation.
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+
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+ -----------------------------------------------------------------------------------------------
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+ Longitudinal Segmentation
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+ -a1 longitudinal model (0 - developmental; 1 - plasticity/learning; 2 - aging; 3 - save models 1 and 2)
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+ -a2 TPM
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+ -----------------------------------------------------------------------------------------------
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+ cat_standalone.sh -s $SPMROOT -m /Applications/MATLAB/MATLAB_Runtime/v93 \
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+ -b ${cwd}/cat_standalone_segment_long.m sTRIO000*.nii \
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+ -a1 "2"
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+ Preprocess (segment) the files sTRIO000*.nii with the longitudinal pipeline optimized for
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+ detecting aging/developmental effects. In order to choose the longitudinal model optimized for
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+ detecting small changes due to plasticity/learning change the a1 parameter to "1".
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+
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+ cat_standalone.sh -s $SPMROOT -m /Applications/MATLAB/MATLAB_Runtime/v93 \
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+ -b ${cwd}/cat_standalone_segment_long.m sTRIO000*.nii \
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+ -a1 "1" -a2 " '${cat12_dir}/templates_MNI152NLin2009cAsym/TPM_Age11.5.nii' "
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+ Preprocess (segment) the files sTRIO000*.nii with the longitudinal pipeline optimized for
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+ detecting plasticity/learning effects and use the children TPM provided with CAT12.
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+ Please note the multiple quotes for parameter a2.
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+
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+ -----------------------------------------------------------------------------------------------
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+ Segmentation (Simple Mode)
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+ -----------------------------------------------------------------------------------------------
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+ cat_standalone.sh -s $SPMROOT -m /Applications/MATLAB/MATLAB_Runtime/v93 \
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+ -b ${cwd}/cat_standalone_simple.m sTRIO0001.nii
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+ Process the single file sTRIO0001.nii using the simple processing batch.
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+
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+ -----------------------------------------------------------------------------------------------
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+ Resample & Smooth Surfaces
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+ -a1 smoothing filter size surface values
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+ -a2 use 32k mesh from HCP (or 164k mesh from Freesurfer)
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+ -----------------------------------------------------------------------------------------------
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+ cat_standalone.sh -s $SPMROOT -m /Applications/MATLAB/MATLAB_Runtime/v93 \
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+ -b ${cwd}/cat_standalone_resample.m lh.thickness.sTRIO0001 \
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+ -a1 "12" -a2 "1"
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+ Resample and smooth the single thickness file lh.thickness.sTRIO0001 with 12mm and save the
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+ resampled mesh as 32k mesh (HCP conform mesh). Only the left surface file has to be defined.
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+ The right hemisphere is processed automatically.
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+
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+ -----------------------------------------------------------------------------------------------
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+ Smoothing
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+ -a1 smoothing filter size
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+ -a2 prepending string for smoothed file (e.g. 's6')
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+ -----------------------------------------------------------------------------------------------
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+ cat_standalone.sh -s $SPMROOT -m /Applications/MATLAB/MATLAB_Runtime/v93 \
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+ -b ${cwd}/cat_standalone_smooth.m sTRIO*nii \
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+ -a1 "[6 6 6]" -a2 " 's6' "
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+ Smooth the volume files sTRIO*nii with 6mm and prepend the string "s6" to the smoothed files.
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+ Please note the multiple quotes for parameter a2.
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+
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+ -----------------------------------------------------------------------------------------------
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+ Dicom Import
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+ -a1 directory structure
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+ -a2 output directory
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+ -----------------------------------------------------------------------------------------------
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+ cat_standalone.sh -s $SPMROOT -m /Applications/MATLAB/MATLAB_Runtime/v93 \
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+ -b ${cwd}/cat_standalone_dicom2nii.m *.dcm \
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+ -a1 " 'patid_date' " -a2 "{'converted'}"
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+ Import DICOM files *.dcm and save converted nifti files in directory "converted" with structure
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+ ./<PatientID>/<StudyDate-StudyTime>/<ProtocollName>
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+ Other options for directory structure are:
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+ 'flat' No directory hierarchy
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+ 'series' ./<ProtocollName>
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+ 'patid_date' ./<PatientID>/<StudyDate-StudyTime>/<ProtocollName>
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+ 'patid' ./<PatientID>/<ProtocollName>
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+ 'date_time' ./<StudyDate-StudyTime>/<ProtocollName>
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+ Please note the multiple quotes for parameter a1.
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+
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+ -----------------------------------------------------------------------------------------------
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+ De-Facing
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+ -----------------------------------------------------------------------------------------------
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+ cat_standalone.sh -s $SPMROOT -m /Applications/MATLAB/MATLAB_Runtime/v93 \
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+ -b ${cwd}/cat_standalone_deface.m sTRIO*.nii
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+ Apply de-facing to sTRIO*.nii and save the files prefixed by "anon_".
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+
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+ -----------------------------------------------------------------------------------------------
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+ Estimate and Save Quality Measures for Volumes or Surfaces
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+ -a1 csv output filename
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+ -a2 enable global scaling with TIV (only for volumes meaningful)
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+ -----------------------------------------------------------------------------------------------
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+ cat_standalone.sh -s $SPMROOT -m /Applications/MATLAB/MATLAB_Runtime/v93 \
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+ -b ${cwd}/cat_standalone_get_quality.m mwp1sTRIO*nii \
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+ -a1 " 'Quality_measures.csv' " -a2 "1"
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+ Estimate mean z-scores using global scaling with TIV for the files mwp1sTRIO*nii and save quality
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+ measures in Quality_measures.csv for external analysis. Processing of surface meshes is also
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+ supported.
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+ Please note the multiple quotes for parameter a1.
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+
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+ -----------------------------------------------------------------------------------------------
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+ Estimate mean/volume inside ROI
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+ -a1 output-file string
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+ -----------------------------------------------------------------------------------------------
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+ cat_standalone.sh -s $SPMROOT -m /Applications/MATLAB/MATLAB_Runtime/v93 \
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+ -b ${cwd}/cat_standalone_get_ROI_values.m catROI_*.xml \
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+ -a1 " 'ROI' "
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+ Save mean volume values in mL (e.g. GM volume) or the mean surface values (e.g. thickness) for
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+ all data catROI_*.xml in a csv-file. The csv-file is named "ROI_" followed by the atlas name
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+ and the name of the measure (e.g. Vgm).
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+ Please note the multiple quotes for parameter a1.
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+
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+ -----------------------------------------------------------------------------------------------
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+ TFCE Statistical Estimation
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+ -a1 contrast number
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+ -a2 number of permutations
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+ -----------------------------------------------------------------------------------------------
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+ cat_standalone.sh -s $SPMROOT -m /Applications/MATLAB/MATLAB_Runtime/v93 \
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+ -b ${cwd}/cat_standalone_tfce.m SPM.mat \
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+ -a1 "2" -a2 "20000"
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+ Call estimation of TFCE statistics for the given SPM.mat file for contrast number 2 with 20000
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+ permutations.
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+
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+ -----------------------------------------------------------------------------------------------
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+ Parallelization
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+ -----------------------------------------------------------------------------------------------
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+ cat_parallelize.sh -p 8 -l /tmp \
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+ -c "cat_standalone.sh -s $SPMROOT -m /Applications/MATLAB/MATLAB_Runtime/v93 -b ${cwd}/cat_standalone_segment.m" sTRIO*.nii
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+ Parallelize CAT12 preprocessing by splitting all sTRIO*.nii files into 8 jobs
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+ (processes) and save log file in /tmp folder.
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+
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+ The parameters SPMROOT and MCRROOT have to be defined (exported) to skip the use of the flags -s -m.
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+
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+INPUT:
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+ nifti files or surface data
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+
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+OUTPUT:
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+ processed images and optionally surfaces according to settings in cat_standalone_*.m
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+
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+USED FUNCTIONS:
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+ cat_parallelize.sh
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+ SPM12 standalone version (compiled)
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+ CAT12 toolbox (compiled within SPM12 if installed)
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+ MATLAB Compiler Runtime R2017b (Version 9.3)
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+
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+This script was written by Christian Gaser (christian.gaser@uni-jena.de).
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+This is ${version}.
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+
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+
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+Known issues:
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+
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+- Parallelization with cat_parallelize.sh is not implemented yet.
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+- Longitudinal segmentation with cat_standalone_segment_long.m
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+ is not tested yet.
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+
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+
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+Contact information:
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+
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+Any problems or concerns regarding this container should be reported
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+to Malgorzata Wierzba (m.wierzba@fz-juelich.de), Michael Hanke
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+(m.hanke@fz-juelich.de) or Felix Hoffstaedter (f.hoffstaedter@fz-juelich.de)
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+
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+
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+Acknowledgements:
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+
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+The CAT toolbox (http://www.neuro.uni-jena.de/cat) is developed by
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+Christian Gaser and Robert Dahnke (Jena University Hospital,
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+Departments of Psychiatry and Neurology) and is free but copyright
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+software, distributed under the terms of the GNU General Public
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+Licence.
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+
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+The SPM software (https://www.fil.ion.ucl.ac.uk/spm/) is developed by
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+the Wellcome Trust Centre for Neuroimaging and is free but copyright
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+software, distributed under the terms of the GNU General Public
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+Licence.
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+
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+MATLAB Compiler Runtime
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+(https://uk.mathworks.com/products/compiler/matlab-runtime.html) is
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+developed by the The MathWorks, Inc. and is subject to the MATLAB
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+Runtime licence.
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