robertoostenveld
commented
5 years ago I am fine with deleting the old documentation from the markdown files. It can be found and retrieved using "git log" etc.
Regarding making the pipeline available: we indeed had a scaffold on http://github.com/Donders-Institute, but since it never contained any real code, I deleted it some time ago. How about making it available in fieldtrip/bin? Or in fieldtrip/contrib?
This is actually a mixed fieldtrip/fieldtrip and fieldtrip/website issue.
I have been recently explaining how to create surface based sourcemodels using an adjusted version of HCP's postfreesurferscript functionality. This inspired me to now finally document this properly (and deprecate the MNE-suite based explanation, which by the way requires quite some fiddlig around to get it running anyway).
-given the fact that the website is now git based, it feels OK to me to get rid of the old description altogether, rather than moving it elsewhere (what do you think @robertoostenveld ?): otherwise move the old description to another meaningful location -streamline the anatomy pipeline code -upgrade to the latest version of freesurfer and test its functionality (using Subject01) (6.0, which possible yields more robust skullstrips, which would get rid of the requirement to do the skullstripping with spm or fsl, and makes the pipeline less 'complicated'). -ensure that the template low-res spherical meshes are in the template directory -update the description in the tutorial as per the data flow in the pipeline. -make the pipeline code available. Question: how to best do this? Especially, the postfreesurferscript is quite elaborate, and too elaborate to paste on the website. Didn't we use to have a scaffold for a pipeline repository on the Donders-Institute github? This would be a possilbe location to store for in house use.