Difference between revisions of "NiftyPipe"
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NiftyPipe is installed as part of NifTK (or NiftyMIDAS) and requires to have python set to use nipype. | NiftyPipe is installed as part of NifTK (or NiftyMIDAS) and requires to have python set to use nipype. | ||
You can find more information about the nipype package on [http://nipy.org/nipype this page] | You can find more information about the nipype package on [http://nipy.org/nipype this page] | ||
| + | |||
| + | __FORCETOC__ | ||
| + | __TOC__ | ||
<h1>Using NiftyPipe on the Computer Science cluster</h1> | <h1>Using NiftyPipe on the Computer Science cluster</h1> | ||
The nipype enabled python version can be find here: <code>/share/apps/cmic/nipype</code> | The nipype enabled python version can be find here: <code>/share/apps/cmic/nipype</code> | ||
| − | We recommend to add the following | + | We recommend to add the following lines to your <code>~/.bashrc</code> file. |
<pre> | <pre> | ||
export PATH=/share/apps/cmic/nipype/bin:${PATH} | export PATH=/share/apps/cmic/nipype/bin:${PATH} | ||
| − | export LD_LIBRARY_PATH=/share/apps/cmic/nipype/ | + | export LD_LIBRARY_PATH=/share/apps/cmic/nipype/lib:${LD_LIBRARY_PATH} |
</pre> | </pre> | ||
| Line 21: | Line 24: | ||
<h1>Using NiftyPipe on the DRC network</h1> | <h1>Using NiftyPipe on the DRC network</h1> | ||
The nipype enabled python version can be find here: <code>/var/drc/software/64bit/nipype</code> | The nipype enabled python version can be find here: <code>/var/drc/software/64bit/nipype</code> | ||
| − | + | Add the following lines to your <code>~/.bash_profile</code> file towards the end. | |
<pre> | <pre> | ||
export PATH=/var/drc/software/64bit/nipype/bin:${PATH} | export PATH=/var/drc/software/64bit/nipype/bin:${PATH} | ||
| − | export | + | export PATH=/var/drc/software/64bit/niftymidas-nightly/bin:${PATH} |
| + | export PATH=/var/drc/software/64bit/niftymidas-nightly/python:${PATH} | ||
| + | export PYTHONPATH=/var/drc/software/64bit/niftymidas-nightly/python:${PYTHONPATH} | ||
</pre> | </pre> | ||
| + | This will ensure that you use the latest and correct version of the different scripts and software (niftireg/niftyseg/etc) necessary for the pipelines. Note that you need extra software if you are using the dti groupwise/tbss/regional-analysis as it needs dti-tk which is not installed in the DRC network by default. | ||
| − | + | The pipelines are now in your PATH so you will be able to call them directly, e.g: | |
<pre> | <pre> | ||
| − | + | perform_dti_processing_drc_protocol.py -m <MIDAS_code> -o output_dir | |
| − | + | ||
</pre> | </pre> | ||
| + | |||
| + | Please refer to [[NiftyPipe documentation]] for documentation of the different pipelines. | ||
Latest revision as of 09:09, 23 November 2015
Description of NiftyPipe
NiftyPipe is installed as part of NifTK (or NiftyMIDAS) and requires to have python set to use nipype. You can find more information about the nipype package on this page
Contents
Using NiftyPipe on the Computer Science cluster
The nipype enabled python version can be find here: /share/apps/cmic/nipype
We recommend to add the following lines to your ~/.bashrc file.
export PATH=/share/apps/cmic/nipype/bin:${PATH}
export LD_LIBRARY_PATH=/share/apps/cmic/nipype/lib:${LD_LIBRARY_PATH}
Kirsi, for the time being, I installed the latest NiftyPipe version in /share/apps/cmic/niftypipe and you should set the PYTHONPATH variable to /share/apps/cmic/niftypipe/python by using:
export PYTHONPATH=/share/apps/cmic/niftypipe/python:${PYTHONPATH}
export PATH=/share/apps/cmic/niftypipe/python:${PATH}
Using NiftyPipe on the DRC network
The nipype enabled python version can be find here: /var/drc/software/64bit/nipype
Add the following lines to your ~/.bash_profile file towards the end.
export PATH=/var/drc/software/64bit/nipype/bin:${PATH}
export PATH=/var/drc/software/64bit/niftymidas-nightly/bin:${PATH}
export PATH=/var/drc/software/64bit/niftymidas-nightly/python:${PATH}
export PYTHONPATH=/var/drc/software/64bit/niftymidas-nightly/python:${PYTHONPATH}
This will ensure that you use the latest and correct version of the different scripts and software (niftireg/niftyseg/etc) necessary for the pipelines. Note that you need extra software if you are using the dti groupwise/tbss/regional-analysis as it needs dti-tk which is not installed in the DRC network by default.
The pipelines are now in your PATH so you will be able to call them directly, e.g:
perform_dti_processing_drc_protocol.py -m <MIDAS_code> -o output_dir
Please refer to NiftyPipe documentation for documentation of the different pipelines.
