Difference between revisions of "NiftyPipe"
| Line 5: | Line 5: | ||
<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} | ||
| Line 21: | Line 21: | ||
<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> | ||
| − | We recommend to add the following | + | We recommend to add the following lines to your <code>~/.bash_profile</code> file. |
<pre> | <pre> | ||
export PATH=/var/drc/software/64bit/nipype/bin:${PATH} | export PATH=/var/drc/software/64bit/nipype/bin:${PATH} | ||
Revision as of 08:25, 27 August 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
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:${PATH}
export LD_LIBRARY_PATH=/share/apps/cmic/nipype/bin:${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
We recommend to add the following lines to your ~/.bash_profile file.
export PATH=/var/drc/software/64bit/nipype/bin:${PATH}
export LD_LIBRARY_PATH=/var/drc/software/64bit/nipype/bin:${LD_LIBRARY_PATH}
Kirsi, for the time being, I installed the latest NiftyPipe version in /var/drc/scratch1/modat/Code/NiftyPipe_install and you should set the PYTHONPATH variable to /var/drc/scratch1/modat/Code/NiftyPipe_install/python by using:
export PYTHONPATH=/var/drc/scratch1/modat/Code/NiftyPipe_install/python:${PYTHONPATH}
export PATH=/var/drc/scratch1/modat/Code/NiftyPipe_install/python:${PATH}
