fix link to compiled cat12.7, now r1743 and include build command to README

README.md

@@ -6,11 +6,16 @@ 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)
+- [Computational Anatomy Toolbox](http://www.neuro.uni-jena.de/cat/) (CAT12.7 r1743)
 - 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 build the singularity container:
+
+Execute the built command with root privileges (sudo)
+`singularity build cat-r1743.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).

Singularity

@@ -14,11 +14,12 @@ From: debian:buster-slim
 
     # 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"
+    SPMURL="http://www.neuro.uni-jena.de/cat12/CAT12.7_r1743_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
+    wget "${SPMURL}" && unzip -d /code/SPM CAT12.7_r1743_R2017b_MCR_Linux.zip
+    mv /code/SPM/CAT12.7_r1743_R2017b_MCR_Linux /code/SPM/MCR_Linux/
 
     # install MCR
     /downloads/MCR/install -mode silent -agreeToLicense yes
@@ -36,7 +37,7 @@ From: debian:buster-slim
     # 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
@@ -63,9 +64,9 @@ 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)
+- MATLAB Compiler Runtime (R2017b, 9.3)
+- Standalone version of SPM software (SPM12, r7771)
+- Computational Anatomy Toolbox (CAT12.7 r1743)
 - CAT interface scripts (cat_standalone.sh, cat_parallelize.sh).
 
 For more details on the exact version of the software used in this
@@ -111,11 +112,11 @@ singularity run container.simg copy all $HOME
 
 -- Running CAT --
 
-Run the CAT analysis with the following command: 
+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'): 
+container ('/batch'):
 singularity run --cleanenv container.simg \
 	-b /batch/cat_standalone_segment.txt \
 	T1.nii
@@ -145,23 +146,23 @@ singularity run --cleanenv --bind /data:/mnt container.simg \
 
 EXAMPLES:
 
-CAT12 segmentation batch: 
+CAT12 segmentation batch:
 singularity run --cleanenv container.simg \
 	-b cat_standalone_segment.txt \
 	T1.nii
 
-CAT12 simple processing batch: 
+CAT12 simple processing batch:
 singularity run --cleanenv container.simg \
 	-b cat_standalone_simple.txt \
 	T1.nii
 
-CAT12 resample & smooth batch: 
+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: 
+CAT12 volume smoothing batch:
 singularity run --cleanenv container.simg \
 	-b cat_standalone_smooth.txt \
 	-a1 "[6 6 6]" -a2 "'s6'" \
@@ -171,7 +172,7 @@ singularity run --cleanenv container.simg \
 Known issues:
 
 - Parallelization with cat_parallelize.sh is not implemented yet.
-- Longitudinal segmentation with cat_standalone_segment_long.txt 
+- Longitudinal segmentation with cat_standalone_segment_long.txt
   is not tested yet.