Commit 3023e24b authored by Michael Krause's avatar Michael Krause 🎉
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ANTS: update docs, thanks Martin

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Useful \*nix programs Useful \*nix programs
===================== =====================
...@@ -6,6 +7,8 @@ tools to help with you daily workflow. If you have suggestions for awesome ...@@ -6,6 +7,8 @@ tools to help with you daily workflow. If you have suggestions for awesome
tools let me know! tools let me know!
.. _tmux:
tmux tmux
---- ----
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ANTS ANTS
==== ====
We are tracking ANTS from the `Neurodebian`_ repository. To use ANTS add the We used to track ANTs from the `Neurodebian`_ repository, but right now the
installation directory to your environment. This can be conveniently done with package is unavailable and there are some custom compiled environment modules
environment modules: instead.
To use ANTs, you have to add the installation directory to your environment. This can be
done done with environment modules:
.. code-block:: bash .. code-block:: bash
module load ants $ module avail ants
--- /opt/environment/modules ---
There are currently 2 versions of ANTS: ants/2.1.0-mpib0 ants/2.3.3-mpib0 ants/2.3.5-mpib0
+ 2.1.0 from neurodebian.org $ module load ants
+ 2.1.0-mpib0 with some minor patches in Scripts/ for Torque PBS
Afterwards all ants* related programs are in your PATH and ready to use. There Afterwards all ants* related programs are in your PATH and ready to use.
is no implicit job parallelism afaik except for some scripts like ``buildtemplateparallel.sh``.
To use this add the options ``-c 4 -q default`` to the command line: Some of the convenient template building scripts distribute their tasks with
different cluster systems using the ``-c`` switch. To use SLURM you need to
pass ``-c 5`` to these scripts. For example to build a template with
``antsMultivariateTemplateConstruction2.sh`` you could run:
.. code-block:: bash .. code-block:: bash
module load ants module load ants
buildtemplateparallel.sh -d 3 -t GR -c 4 -q default -o ANTS T1*nii antsMultivariateTemplateConstruction2.sh -d 3 -i 3 -k 1 -f 4x2x1 -s 2x1x0vox -q 30x20x4 -t SyN -m CC -o your_prefix -c 5 -j 8 *T1w.nii.gz
Hint: add an optional ``&`` at the end of the line to run the script in the background.
This will run some initial tasks directly on the cluster login node and start
the more work intensive tasks automatically as a SLURM job.
.. note:: .. note::
Some scripts require ``-Q default`` instead of ``-q default``. Check the help page to get the correct parameter. Add an optional ``&`` at the end of the line to run the script in the
background. Alternatively, you could use :ref:`tmux` to start scripts in the
background.
All other programs need to be wrapped into a job file to be run on the cluster nodes: We also track a tiny set of patches on top of the regular scripts (as indicated
with the `-mpibX` suffix). One of the changes in these patches reuses the
``-j`` switch to configure the cores used for each of the template building sub
tasks. Tuning this value further improves running time. The table below lists
a simple benchmark for a template building pipeline using the first
9 subjects from the ds000001 dataset using the ``antsMultivariateTemplateConstruction2.sh``
command shown above.
==== ==============
-j X Time (minutes)
==== ==============
4 70
8 39
16 24
32 15
==== ==============
All other ANTs programs need to be wrapped into a job file to be run on the cluster nodes:
.. code-block:: bash .. code-block:: bash
......
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