NiftyPipe

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:${PATH}
export LD_LIBRARY_PATH=/share/apps/cmic/nipype/lib:${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.