software: update spm to reflect env modules

conf.py

@@ -56,7 +56,7 @@ author = 'Michael'
 # built documents.
 #
 # The short X.Y version.
-version = '3.6.0'
+version = '3.6.1'
 # The full version, including alpha/beta/rc tags.
 release = '3.6.0'
 

index.rst

@@ -4,6 +4,9 @@ Welcome to Tardis's documentation!
 Changelog
 =========
 
+3.6.1 (19.09.2019)
+  + updated SPM12 section (env modules)
+
 3.6 (02.07.2019)
   + added section about Torque Dependencies
 

software/matlab.rst

@@ -175,11 +175,21 @@ version as MCR upon script invocation with :program:`run_project.sh`.
 SPM
 ---
 
-SPM already comes as a pre-compiled version and can, identical to the examples
-above, be started with :program:`run_spm8.sh` or :program:`run_spm12.sh`.
+There are environment modules available to choose from and activate SPM12. At
+the time of writing these are:
+
+
+.. code-block::
+
+   [krause@master ~] module avail spm12
+
+   -------------- /opt/environment/modules ---------------
+   spm12/6225 spm12/6470 spm12/6685 spm12/6906 spm12/7219
+
+
 Usually users are exporting a number of batch files with the spm gui on their
 local machine, change the paths to reflect the names on the tardis and then
-call :program:`run_spm12.sh` with the **run** parameter for each batch file.
+call :program:`run_spm12.sh` with the **batch** parameter for each batch file.
 
 
 Example: segmentation for a number of nifti images. The file batch.template
@@ -195,7 +205,7 @@ template:
    for image in tp2/Old/*.nii ; do
        fullpath=$PWD/$image
        sed "s#%%IMAGE%%#$fullpath#" batch.template > batch_${i}.m
-       echo "run_spm12.sh /opt/matlab/interactive run $PWD/batch_${i}.m" | qsub -d.
+       echo "module load spm12 ; run_spm12.sh /mcr batch $PWD/batch_${i}.m" | qsub -d.
        i=$((i+1))
    done
 
@@ -231,9 +241,9 @@ toolboxes to SPM (e.g. cat12).
    >>
 
 
-This should create a folder :file:`spm_exec` below the spm toolbox location
-containing the fresh :program:`spm12` and :program:`run_spm12.sh` which you can
-then use in your jobs just like above.
+This should create a folder :file:`spm_exec` or :file:`standalone` below the
+spm toolbox location containing the fresh :program:`spm12` and
+:program:`run_spm12.sh` which you can then use in your jobs just like above.
 
 Fieldtrip
 ---------