# CAT container

This container allows to run the standalone, compiled version of the [Computational Anatomy Toolbox (CAT)](http://www.neuro.uni-jena.de/cat/), which is an extension to [SPM](https://www.fil.ion.ucl.ac.uk/spm/software/) software. Using the container does not require the availability of a MATLAB licence.

The container includes:

- [MATLAB Compiler Runtime](https://uk.mathworks.com/products/compiler/matlab-runtime.html) (R2017b, 9.3)
- Standalone version of [SPM](https://www.fil.ion.ucl.ac.uk/spm/software/) software (SPM12, r7771)
- [Computational Anatomy Toolbox](http://www.neuro.uni-jena.de/cat/) (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 recipe 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](http://www.neuro.uni-jena.de/cat12/CAT12-Manual.pdf).

## 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`), for instance:

`singularity run --cleanenv container.simg -b /batch/cat_standalone_segment.txt T1.nii`

To use your own, customised batch file, simply specify its path, for instance:

`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](https://sylabs.io/guides/3.0/user-guide/bind_paths_and_mounts.html#system-defined-bind-paths) 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 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 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 is developed by the The MathWorks, Inc. and is subject to the MATLAB Runtime licence.