Work in Progress!
At the moment this pipeline simply tries so resemble our other, shell-script based, pipeline at http://github.com/BrainModes/TVB-empirical-data-pipeline
The sripts are all included in the notebooks folder, currently as ipython notebooks and py-files.
TVB_pipeline is the "master-control-script" which is later intended to be run via the console (i.e. python TVB_pipeline.py )
To run it on a specific cluster architecture, simply edit the plugin-type in the master control script
- Write a new Documentation!
- Implement fMRI processing based on the code here: https://github.com/BrainModes/TVB-empirical-data-pipeline/blob/NSG/fmriFC.sh
- Implement Tractography Thresholding into the MRTrix module. Possibly trying to include the method described in Morris et al. (2008)
- Make the file-sorting of the user-data more sophisticated. This means that the pipeline should be able to somehow recognize which kinds of data-sets (e.g. fMRI, T1, dwMRI) is included in the user data and then route the particular folder-paths onto the corresponding processing-nodes inside the pipeline. This might be achieved through using nipype's SelectFiles interface
- Include some example workflows for different cluster scenarios, realized through e.g. controll-scripts written in BASH