brainage/More/Singularity_r2042

Bootstrap: docker
From: debian:buster-slim

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

    chmod -R 777 ${SINGULARITY_ROOTFS}/code

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

    # download software & unzip
    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/CAT12.8.1_r2042_R2017b_MCR_Linux.zip"
    SPMURL="http://141.35.69.218/cat12/CAT12.8.1_r2042_R2017b_MCR_Linux.zip"

    cd /downloads
    wget "${MCRURL}" && unzip -d /downloads/MCR MCR_R2017b_glnxa64_installer.zip
    wget "${SPMURL}" && unzip -d /code/SPM CAT12.8.1_r2042_R2017b_MCR_Linux.zip
    

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

    # generalize CAT12 version
    mv /code/SPM/CAT12.8.1_r2042_R2017b_MCR_Linux/ /code/SPM/MCR_Linux/

    # 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 spm12.ctf

    # install CAT standalone interface
    STANDALONE="/code/SPM/MCR_Linux/standalone"
    cd ${STANDALONE} && chmod +rx *.sh
    cd /code && ln -s ${STANDALONE}/*.sh .
    cd /batch && ln -s ${STANDALONE}/*.m .
  
    # set permissions
    find /code -type f -print0 | xargs -0 chmod +r
    find /code/SPM/MCR_Linux/spm12_mcr/ -name 'CAT.glnx86' -print0 | xargs -0 chmod +rx -R
    rm -f code/cat_standalone_segment_enigma.m
    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

    chmod -R 777 /code*

    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
    NOW=$(date +%s)
    exec /code/cat_standalone.sh "$@" 2>&1 |tee cat_$NOW.log

%labels
    Authors Malgorzata Wierzba (m.wierzba@fz-juelich.de)
            Felix Hoffstaedter (f.hoffstaedter@fz-juelich.de)
    Version 1.1

%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 (CAT12.8 r2042)
- 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.m, cat_standalone_simple.m,
cat_standalone_resample.m, cat_standalone_smooth.m) 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.m

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.m $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.m \
	T1.nii

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


EXAMPLES:

USAGE:
   cat_standalone.sh filename(s) [-s spm_standalone_folder] [-m mcr_folder] [-b batch_file]
                                 [-a1 additional_argument1] [-a2 additional_argument2]
                                 [-a add_to_batch]

   -s <DIR>    | --spm <DIR>     SPM12 folder of standalone version (can be also defined by SPMROOT)
   -m <DIR>    | --mcr <DIR>     Matlab Compiler Runtime (MCR) folder (can be also defined by MCRROOT)
   -b <FILE>   | --batch <FILE>  batch file to execute
   -a1 <STRING>| --arg1 <STRING> 1st additional argument (otherwise use defaults or batch)
   -a2 <STRING>| --arg2 <STRING> 2nd additional argument (otherwise use defaults or batch)
   -a <STRING> | --add  <STRING> add option to batch file

   The first occurance of the parameter "<UNDEFINED>" in the batch file will be replaced by the
   list of input files. You can use the existing batch files in this folder or create your own batch
   file with the SPM12 batch editor and leave the data field undefined. Please note that for creating
   your own batch file CAT12 has to be called in expert mode because the CAT12 standalone installation
   will only run in expert mode to allow more options.
   See cat_standalone_segment.m for an example.

   You can also define one or two optional arguments to change other parameters that are indicated by
   "<UNDEFINED>" in the batch file. Please take care of the order of the "<UNDEFINED>" fields in the
   batch file! If no additional arguments are defined the default values are used.
   Also, you must use multiple quotes if the argument is a string (e.g. " 'your_string' ").

   If you use a computer cluster it is recommended to use the batch files to only process one data set
   and use a job or queue tool to call the (single) jobs on the cluster.

PURPOSE:
   Command line call of (CAT12) batch files for SPM12 standalone installation

EXAMPLES
   -----------------------------------------------------------------------------------------------
   Segmentation
     -a1 TPM
     -a2 Shooting template
   -----------------------------------------------------------------------------------------------
   cat_standalone.sh -s $SPMROOT -m /Applications/MATLAB/MATLAB_Runtime/v93 \
       -b ${cwd}/cat_standalone_segment.m sTRIO0001.nii
   Preprocess (segment) the single file sTRIO0001.nii using the default CAT12 preprocessing batch.
   SPM12 standalone version is located in $SPMROOT and Matlab Compiler Runtime in
   /Applications/MATLAB/MATLAB_Runtime/v93.

   cat_standalone.sh -s $SPMROOT -m /Applications/MATLAB/MATLAB_Runtime/v93 \
       -b ${cwd}/cat_standalone_segment.m sTRIO000*.nii.gz \
       -a1 " '${cat12_dir}/templates_MNI152NLin2009cAsym/TPM_Age11.5.nii' " \
       -a2 " '${cat12_dir}/templates_MNI152NLin2009cAsym/Template_0_GS1mm.nii' "
   Unzip and preprocess (segment) the files sTRIO0001.nii.gz using the default CAT12 preprocessing
   batch, but use the children TPM provided with CAT12 and a 1mm Shooting template (not provided
   with CAT12). Please note that zipped file can only be handled with this standalone batch and also
   note the multiple quotes for parameter a1 and a2.

   cat_standalone.sh -s $SPMROOT -m /Applications/MATLAB/MATLAB_Runtime/v93 \
       -b ${cwd}/cat_standalone_segment.m sTRIO0001.nii \
       -a "matlabbatch{1}.spm.tools.cat.estwrite.output.surface = 0;"
   Preprocess (segment) the single file sTRIO0001.nii using the default CAT12 preprocessing batch,
   but skip surface estimation.

   -----------------------------------------------------------------------------------------------
   Longitudinal Segmentation
     -a1 longitudinal model (0 - developmental; 1 - plasticity/learning; 2 - aging; 3 - save models 1 and 2)
     -a2 TPM
   -----------------------------------------------------------------------------------------------
   cat_standalone.sh -s $SPMROOT -m /Applications/MATLAB/MATLAB_Runtime/v93 \
       -b ${cwd}/cat_standalone_segment_long.m sTRIO000*.nii \
       -a1 "2"
   Preprocess (segment) the files sTRIO000*.nii with the longitudinal pipeline optimized for
   detecting aging/developmental effects. In order to choose the longitudinal model optimized for
   detecting small changes due to plasticity/learning change the a1 parameter to "1".

   cat_standalone.sh -s $SPMROOT -m /Applications/MATLAB/MATLAB_Runtime/v93 \
       -b ${cwd}/cat_standalone_segment_long.m sTRIO000*.nii \
       -a1 "1" -a2 " '${cat12_dir}/templates_MNI152NLin2009cAsym/TPM_Age11.5.nii' "
   Preprocess (segment) the files sTRIO000*.nii with the longitudinal pipeline optimized for
   detecting plasticity/learning effects and use the children TPM provided with CAT12.
   Please note the multiple quotes for parameter a2.

   -----------------------------------------------------------------------------------------------
   Segmentation (Simple Mode)
   -----------------------------------------------------------------------------------------------
   cat_standalone.sh -s $SPMROOT -m /Applications/MATLAB/MATLAB_Runtime/v93 \
       -b ${cwd}/cat_standalone_simple.m sTRIO0001.nii
   Process the single file sTRIO0001.nii using the simple processing batch.

   -----------------------------------------------------------------------------------------------
   Resample & Smooth Surfaces
     -a1 smoothing filter size surface values
     -a2 use 32k mesh from HCP (or 164k mesh from Freesurfer)
   -----------------------------------------------------------------------------------------------
   cat_standalone.sh -s $SPMROOT -m /Applications/MATLAB/MATLAB_Runtime/v93 \
       -b ${cwd}/cat_standalone_resample.m lh.thickness.sTRIO0001 \
       -a1 "12" -a2 "1"
   Resample and smooth the single thickness file lh.thickness.sTRIO0001 with 12mm and save the
   resampled mesh as 32k mesh (HCP conform mesh). Only the left surface file has to be defined.
   The right hemisphere is processed automatically.

   -----------------------------------------------------------------------------------------------
   Smoothing
     -a1 smoothing filter size
     -a2 prepending string for smoothed file (e.g. 's6')
   -----------------------------------------------------------------------------------------------
   cat_standalone.sh -s $SPMROOT -m /Applications/MATLAB/MATLAB_Runtime/v93 \
       -b ${cwd}/cat_standalone_smooth.m sTRIO*nii \
       -a1 "[6 6 6]" -a2 " 's6' "
   Smooth the volume files sTRIO*nii with 6mm and prepend the string "s6" to the smoothed files.
   Please note the multiple quotes for parameter a2.

   -----------------------------------------------------------------------------------------------
   Dicom Import
     -a1 directory structure
     -a2 output directory
   -----------------------------------------------------------------------------------------------
   cat_standalone.sh -s $SPMROOT -m /Applications/MATLAB/MATLAB_Runtime/v93 \
       -b ${cwd}/cat_standalone_dicom2nii.m *.dcm \
       -a1 " 'patid_date' " -a2 "{'converted'}"
   Import DICOM files *.dcm and save converted nifti files in directory "converted" with structure
   ./<PatientID>/<StudyDate-StudyTime>/<ProtocollName>
   Other options for directory structure are:
     'flat'       No directory hierarchy
     'series'     ./<ProtocollName>
     'patid_date' ./<PatientID>/<StudyDate-StudyTime>/<ProtocollName>
     'patid'      ./<PatientID>/<ProtocollName>
     'date_time'  ./<StudyDate-StudyTime>/<ProtocollName>
   Please note the multiple quotes for parameter a1.

   -----------------------------------------------------------------------------------------------
   De-Facing
   -----------------------------------------------------------------------------------------------
   cat_standalone.sh -s $SPMROOT -m /Applications/MATLAB/MATLAB_Runtime/v93 \
       -b ${cwd}/cat_standalone_deface.m sTRIO*.nii
   Apply de-facing to sTRIO*.nii and save the files prefixed by "anon_".

   -----------------------------------------------------------------------------------------------
   Estimate and Save Quality Measures for Volumes or Surfaces
     -a1 csv output filename
     -a2 enable global scaling with TIV (only for volumes meaningful)
   -----------------------------------------------------------------------------------------------
   cat_standalone.sh -s $SPMROOT -m /Applications/MATLAB/MATLAB_Runtime/v93 \
       -b ${cwd}/cat_standalone_get_quality.m mwp1sTRIO*nii \
       -a1 " 'Quality_measures.csv' " -a2 "1"
   Estimate mean z-scores using global scaling with TIV for the files mwp1sTRIO*nii and save quality
   measures in Quality_measures.csv for external analysis. Processing of surface meshes is also
   supported.
   Please note the multiple quotes for parameter a1.

   -----------------------------------------------------------------------------------------------
   Estimate mean/volume inside ROI
     -a1 output-file string
   -----------------------------------------------------------------------------------------------
   cat_standalone.sh -s $SPMROOT -m /Applications/MATLAB/MATLAB_Runtime/v93 \
       -b ${cwd}/cat_standalone_get_ROI_values.m catROI_*.xml \
       -a1 " 'ROI' "
   Save mean volume values in mL (e.g. GM volume) or the mean surface values (e.g. thickness) for
   all data catROI_*.xml in a csv-file. The csv-file is named "ROI_" followed by the atlas name
   and the name of the measure (e.g. Vgm).
   Please note the multiple quotes for parameter a1.

   -----------------------------------------------------------------------------------------------
   TFCE Statistical Estimation
     -a1 contrast number
     -a2 number of permutations
   -----------------------------------------------------------------------------------------------
   cat_standalone.sh -s $SPMROOT -m /Applications/MATLAB/MATLAB_Runtime/v93 \
       -b ${cwd}/cat_standalone_tfce.m SPM.mat \
       -a1 "2" -a2 "20000"
   Call estimation of TFCE statistics for the given SPM.mat file for contrast number 2 with 20000
   permutations.

   -----------------------------------------------------------------------------------------------
   Parallelization
   -----------------------------------------------------------------------------------------------
   cat_parallelize.sh -p 8 -l /tmp \
       -c "cat_standalone.sh  -s $SPMROOT -m /Applications/MATLAB/MATLAB_Runtime/v93 -b ${cwd}/cat_standalone_segment.m" sTRIO*.nii
   Parallelize CAT12 preprocessing by splitting all sTRIO*.nii files into 8 jobs
   (processes) and save log file in /tmp folder.

   The parameters SPMROOT and MCRROOT have to be defined (exported) to skip the use of the flags -s -m.

INPUT:
   nifti files or surface data

OUTPUT:
   processed images and optionally surfaces according to settings in cat_standalone_*.m

USED FUNCTIONS:
   cat_parallelize.sh
   SPM12 standalone version (compiled)
   CAT12 toolbox (compiled within SPM12 if installed)
   MATLAB Compiler Runtime R2017b (Version 9.3)

This script was written by Christian Gaser (christian.gaser@uni-jena.de).
This is ${version}.


Known issues:

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


Contact information:

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