Commit 2a15d3b4 authored by Michael Krause's avatar Michael Krause 🎉
Browse files

software: update spm to reflect env modules

parent c6ec9af0
Pipeline #3563 passed with stages
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......@@ -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'
......
......@@ -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
......
......@@ -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
---------
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