I am a researcher at University of Montreal, and one of the organizer of the brainhack school. Each year, I start a project at brainhack school. In general, I don't get to do much on it, because I am busy with other things. But I keep trying.
I have been the lead developper of a tool called Neuroimaging Analysis Kit which includes a few pipelienes for fMRI data processing. The preprocessing pipeline in particular is quite useful. Two main strength of that package: tt's based on Octave and the minc tools, with very liberal licenses, allowing for commercial use (MIT and BSD-like). It's also quite robust, and it's possible to reach high success rate on most datasets with minimum tweaking, and the necessary tweaking is relatively well documented. NIAK was included in the BIDS-app catalogue and the CBRAIN portal, but these implementations were not actively maintained and tested. They are, at that point, broken. Support for BIDS in NIAK is also broken. Despite that, I expect the tool to remain used in my lab and by collaborators for a few years, and fixing all the issues I just mentioned would help make NIAK much more usable.
I'd like to use the new boutiques standard to create a command-line version of niak, which is going to be compatible with the BIDS standard. I would then want to register a new NIAK-fmri-preprocessing pipeline as a BIDS app and also on the CBRAIN portal.
- Boutiques for wrapping tools
- pybids to parse BIDS datasets
- Use Boutiques to generate a BIDS app
- Use Boutiques to generate a CBRAIN app
- A new niak release
- An octave/matlab interface to pybids
- A (working) BIDS app
- A (working) CBRAIN app
- Update NIAK website
- twitter thread