Commit 5f79dfe6 authored by Michael Krause's avatar Michael Krause 🎉
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ANTS: update docs, thanks Martin

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.. _tmux:
Useful \*nix programs
=====================
......
ANTS
====
We are tracking ANTS from the `Neurodebian`_ repository. To use ANTS add the
installation directory to your environment. This can be conveniently done with
environment modules:
We used to track ANTs from the `Neurodebian`_ repository, but right now the
package is unavailable and there are some custom compiled 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
module load ants
There are currently 2 versions of ANTS:
$ module avail ants
--- /opt/environment/modules ---
ants/2.1.0-mpib0 ants/2.3.3-mpib0 ants/2.3.5-mpib0
+ 2.1.0 from neurodebian.org
+ 2.1.0-mpib0 with some minor patches in Scripts/ for Torque PBS
$ module load ants
Afterwards all ants* related programs are in your PATH and ready to use. There
is no implicit job parallelism afaik except for some scripts like ``buildtemplateparallel.sh``.
Afterwards all ants* related programs are in your PATH and ready to use.
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
module load ants
buildtemplateparallel.sh -d 3 -t GR -c 4 -q default -o ANTS T1*nii
Hint: add an optional ``&`` at the end of the line to run the script in the background.
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
This will run some initial taks on the cluster login node and start the more
work intensive taks automatically as a SLURM job.
.. note::
Some scripts require ``-Q default`` instead of ``-q default``. Check the help page to get the correct parameter.
All other programs need to be wrapped into a job file to be run on the cluster nodes:
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.
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
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