cat12-container/Singularity

Bootstrap: docker
From: debian:buster-slim

%setup
    mkdir -p ${SINGULARITY_ROOTFS}/batch
    mkdir -p ${SINGULARITY_ROOTFS}/code
    mkdir -p ${SINGULARITY_ROOTFS}/downloads

    install -m 755 ./code/* ${SINGULARITY_ROOTFS}/code

%post
    apt-get update
    apt-get -y install wget unzip libxext6 libxt6 moreutils

    # download software
    MCRURL="https://ssd.mathworks.com/supportfiles/downloads/R2017b/deployment_files/R2017b/installers/glnxa64/MCR_R2017b_glnxa64_installer.zip"
    SPMURL="http://www.neuro.uni-jena.de/cat12/cat12_latest_R2017b_MCR_Linux.zip"

    cd /downloads
    wget "${MCRURL}" && unzip -d /downloads/MCR MCR_R2017b_glnxa64_installer.zip
    wget "${SPMURL}" && unzip -d /code/SPM cat12_latest_R2017b_MCR_Linux.zip

    # install MCR
    /downloads/MCR/install -mode silent -agreeToLicense yes

    # install SPM
    /code/SPM/MCR_Linux/run_spm12.sh /usr/local/MATLAB/MATLAB_Runtime/v93 quit
    cd /code/SPM/MCR_Linux && chmod +rx run_spm12.sh spm12.sh spm12

    # install CAT standalone interface
    STANDALONE="/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/standalone"
    cd ${STANDALONE} && chmod +rx *.sh
    cd /code && ln -s ${STANDALONE}/*.sh .
    cd /batch && ln -s ${STANDALONE}/*.txt .

    # set permissions
    find /code -type f -print0 | xargs -0 chmod +r
    find /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/CAT.glnx86 -type f -print0 | xargs -0 chmod +rx
 
    rm -fr /downloads

    apt-get clean
    apt-get autoremove

%environment
    export SPMROOT=/code/SPM/MCR_Linux
    export MCRROOT=/usr/local/MATLAB/MATLAB_Runtime/v93
    export MCR_INHIBIT_CTF_LOCK=1

%runscript
    exec /code/main "$@"

%labels
    Author Malgorzata Wierzba (m.wierzba@fz-juelich.de)
    Version 1.0.1

%help

This container allows to run the standalone, compiled version of the
Computational Anatomy Toolbox (CAT), which is an extension to SPM
software. Using the container does not require the availability of a
MATLAB licence.

The container includes:

- MATLAB Compiler Runtime (R2017b, 9.3) 
- Standalone version of SPM software (SPM12, r7771) 
- Computational Anatomy Toolbox (CAT12.7-RC2 r1720)
- CAT interface scripts (cat_standalone.sh, cat_parallelize.sh).

For more details on the exact version of the software used in this
container, please refer to the README file.


HOW TO USE:

In principle this container allows you to perform the very same types
of analysis that are possible with the standalone version of CAT. It
is assumed that the user is familiar with the content of the batch
files dedicated for the use with the standalone version of CAT
(cat_standalone_segment.txt, cat_standalone_simple.txt,
cat_standalone_resample.txt, cat_standalone_smooth.txt) and can modify
their content according to his/her needs. For more details, please
refer to the CAT12 documentation and manual.


-- Available batch files --

The content of the batch files can be explored by using the 'view' and
'copy' subcommands:

singularity run <container> <subcommand> <batch file> <arguments>

To view a batch file, use the 'view' subcommand:

singularity run container.simg view cat_standalone_smooth.txt

To copy a batch file to your computer, use the 'copy' subcommand and
specify destination path as an additional argument:

singularity run container.simg copy cat_standalone_smooth.txt $HOME

Make sure that the specified path is mounted to the container (more
information on this can be found below) and that you have write access
to this path!

To copy all available batch files, use the 'all' argument:

singularity run container.simg copy all $HOME


-- Running CAT --

Run the CAT analysis with the following command: 
singularity run --cleanenv <container> <batch file> <arguments>

To use a default batch file, use one of the files included in the
container ('/batch'): 
singularity run --cleanenv container.simg \
	-b /batch/cat_standalone_segment.txt \
	T1.nii

To use your own, customised batch file, simply specify its path:
singularity run --cleanenv container.simg \
	-b $HOME/cat_standalone_segment.txt \
	T1.nii


-- Bind paths --

Please note that most of the host files remain inaccessible from within
the container. By default the following directories are mounted within
the container: '$HOME', '/tmp', '/proc', '/sys', '/dev', and '$PWD'
(see the Singularity documentation for more details).

If you want the container to be able to access other locations,
specify a bind path of your choice. For instance, to make the contents
of the '/data' folder on your computer available in the '/mnt' folder
inside the container, specify the mount point in the following way:

singularity run --cleanenv --bind /data:/mnt container.simg \
	-b /batch/cat_standalone_segment.txt \
	/mnt/T1.nii


EXAMPLES:

CAT12 segmentation batch: 
singularity run --cleanenv container.simg \
	-b cat_standalone_segment.txt \
	T1.nii

CAT12 simple processing batch: 
singularity run --cleanenv container.simg \
	-b cat_standalone_simple.txt \
	T1.nii

CAT12 resample & smooth batch: 
singularity run --cleanenv container.simg \
	-b cat_standalone_resample.txt \
	-a1 "12" -a2 "1" \
	lh.thickness.T1

CAT12 volume smoothing batch: 
singularity run --cleanenv container.simg \
	-b cat_standalone_smooth.txt \
	-a1 "[6 6 6]" -a2 "'s6'" \
	T1.nii


Known issues:

- Parallelization with cat_parallelize.sh is not implemented yet.
- Longitudinal segmentation with cat_standalone_segment_long.txt 
  is not tested yet.


Contact information:

Any problems or concerns regarding this container should be reported
to Malgorzata Wierzba (m.wierzba@fz-juelich.de) or Michael Hanke
(m.hanke@fz-juelich.de).


Acknowledgements:

The CAT toolbox (http://www.neuro.uni-jena.de/cat) is developed by
Christian Gaser and Robert Dahnke (Jena University Hospital,
Departments of Psychiatry and Neurology) and is free but copyright
software, distributed under the terms of the GNU General Public
Licence.

The SPM software (https://www.fil.ion.ucl.ac.uk/spm/) is developed by
the Wellcome Trust Centre for Neuroimaging and is free but copyright
software, distributed under the terms of the GNU General Public
Licence.

MATLAB Compiler Runtime
(https://uk.mathworks.com/products/compiler/matlab-runtime.html) is
developed by the The MathWorks, Inc. and is subject to the MATLAB
Runtime licence.