@@ -159,15 +159,13 @@ version as MCR upon script invocation with :program:`run_project.sh`.
...
@@ -159,15 +159,13 @@ version as MCR upon script invocation with :program:`run_project.sh`.
1.8339 0.3188 0.3426
1.8339 0.3188 0.3426
-2.2588 -1.3077 3.5784
-2.2588 -1.3077 3.5784
[krause@master ~]
.. note::
.. note::
You only have to compile your project once and can then use it any number
You only have to compile your project once and can then use it any number
of times. Matlab extracts your package to a shared hidden folder called
of times. Matlab extracts your package to a shared hidden folder called
`.mcrCache<Version-Number>`. Those folders sometimes get corrupted by
`.mcrCache<Version-Number>`. Those folders sometimes get corrupted by
Matlab, especially when multiple jobs start at exactly the same time. The
Matlab, especially when multiple jobs start at exactly the same time. The
only workaround so far is to add a sleep 1s between qsub calls and hope
only workaround so far is to add a sleep 1s between qsub/sbatch calls and hope
there is no collision. Also, it makes sense to regularly remove those
there is no collision. Also, it makes sense to regularly remove those
directories. But make sure all your jobs have finished before removing
directories. But make sure all your jobs have finished before removing
them with :file:`rm -rf .mcrCache*`.
them with :file:`rm -rf .mcrCache*`.
...
@@ -176,10 +174,10 @@ SPM
...
@@ -176,10 +174,10 @@ SPM
---
---
SPM already comes as a pre-compiled version and can, identical to the examples
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`. Usually users are
above, be started with :program:`run_spm12.sh`.
exporting a number of batch files with the spm gui on their local machine,
Usually users are exporting a number of batch files with the spm gui on their
change the paths to reflect the names on the tardis and then call
local machine, change the paths to reflect the names on the tardis and then
:program:`run_spm12.sh` with the **run** parameter for each batch file.
call :program:`run_spm12.sh` with the **run** parameter for each batch file.
Example: segmentation for a number of nifti images. The file batch.template contains the string :`%%IMAGE%%` as a placeholder so we can easily replace it with the current image path and create a number of new batches from a single template:
Example: segmentation for a number of nifti images. The file batch.template contains the string :`%%IMAGE%%` as a placeholder so we can easily replace it with the current image path and create a number of new batches from a single template:
...
@@ -192,7 +190,7 @@ Example: segmentation for a number of nifti images. The file batch.template cont
...
@@ -192,7 +190,7 @@ Example: segmentation for a number of nifti images. The file batch.template cont
for image in tp2/Old/*.nii ; do
for image in tp2/Old/*.nii ; do
fullpath=$PWD/$image
fullpath=$PWD/$image
sed "s#%%IMAGE%%#$fullpath#" batch.template > batch_${i}.m
sed "s#%%IMAGE%%#$fullpath#" batch.template > batch_${i}.m
echo "run_spm12.sh /opt/matlab/interactive run $PWD/batch_${i}.m" | qsub -d.
sbatch --wrap "run_spm12.sh /opt/matlab/interactive run $PWD/batch_${i}.m"
i=$((i+1))
i=$((i+1))
done
done
...
@@ -203,7 +201,7 @@ toolboxes to SPM (e.g. cat12).
...
@@ -203,7 +201,7 @@ toolboxes to SPM (e.g. cat12).
.. code-block:: matlab
.. code-block:: matlab
[krause@master ~] matlab
matlab
Warning: No display specified. You will not be able to display graphics on the screen.
Warning: No display specified. You will not be able to display graphics on the screen.
