adjust README

README.md

@@ -4,9 +4,9 @@ This container allows to run the standalone, compiled version of the [Computatio
 
 The container includes:
 
-- [MATLAB Compiler Runtime](https://uk.mathworks.com/products/compiler/matlab-runtime.html) (R2017b, 9.3)
+- GNU Octave (7.3.0)
 - 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 r1743)
+- [Computational Anatomy Toolbox](http://www.neuro.uni-jena.de/cat/) (CAT12.9 r2560)
 - 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.
@@ -15,11 +15,11 @@ For more details on the exact version of the software used in this container, pl
 
 Execute the built command with root privileges:
 
-`sudo singularity build container.simg Singularity`
+`sudo singularity build cat12.9_octave.simg Singularity`
 
 ## 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).
+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](https://neuro-jena.github.io/cat12-help).
 
 ## Available batch files:
 
@@ -29,17 +29,17 @@ The content of the batch files can be explored by using the `view` and `copy` su
 
 To view a batch file, use the `view` subcommand:
 
-`singularity run container.simg view cat_standalone_smooth.txt`
+`singularity run cat12.9_octave.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.txt $HOME`
+`singularity run cat12.9_octave.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`
+`singularity run cat12.9_octave.simg copy all $HOME`
 
 ## Running CAT:
 
@@ -49,11 +49,11 @@ Run the CAT analysis with the following command:
 
 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`
+`singularity run --cleanenv cat12.9_octave.simg -b /batch/cat_standalone_segment.m 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`
+`singularity run --cleanenv cat12.9_octave.simg -b $HOME/cat_standalone_segment.m T1.nii`
 
 ## Bind paths:
 
@@ -61,37 +61,36 @@ Please note that most of the host files remain inaccessible from within the cont
 
 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`
+`singularity run --cleanenv --bind /data:/mnt cat12.9_octave.simg -b /batch/cat_standalone_segment.m /mnt/T1.nii`
 
 ## Examples:
 
 CAT12 segmentation batch:
 
-`singularity run --cleanenv container.simg -b cat_standalone_segment.txt T1.nii`
+`singularity run --cleanenv cat12.9_octave.simg -b cat_standalone_segment.m T1.nii`
 
 CAT12 simple processing batch:
 
-`singularity run --cleanenv container.simg -b cat_standalone_simple.txt T1.nii`
+`singularity run --cleanenv cat12.9_octave.simg -b cat_standalone_simple.m T1.nii`
 
 CAT12 resample & smooth batch:
 
-`singularity run --cleanenv container.simg -b cat_standalone_resample.txt -a1 "12" -a2 "1" lh.thickness.T1`
+`singularity run --cleanenv cat12.9_octave.simg -b cat_standalone_resample.m -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`
+`singularity run --cleanenv cat12.9_octave.simg -b cat_standalone_smooth.m -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.
+* 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) or Michael Hanke (m.hanke@fz-juelich.de).
-
+Any problems or concerns regarding this container should be reported to Felix Hoffstaedter (f.hoffstaedter@fz-juelich.de) and regarding CAT12 to Christian Gaser (christian.gaser@uni-jena.de)  
 
 ## Acknowledgements:
 
@@ -99,4 +98,4 @@ The CAT toolbox is developed by Christian Gaser and Robert Dahnke (Jena Universi
 
 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.
+GNU Octave is a freely redistributable software under the terms of the GPL as published by the Free Software Foundation.