I’m trying to do some fMRI analysis in a common space (e.g. MNI). I would then like to visualize this analysis using pycortex.
Pycortex does provide some functionality to transform to and from MNI space (wrapping fsl). However, I don’t think it is directly possible to use pycortex to visualize on top of a standard brain, e.g. MNI.
How would one go about doing something like that?
Wouldn’t nilearn.plotting support your needs?
Have you reviewed nilearn’s plotting utilities?
Thanks. I’ll have a look at nilearn.
However I’m trying to do this still using pycortex specifically. Pycortex generates the best looking flat maps out there and offers a lot of flexibility regarding the appearance of the plots. I already extensively use it for all my other analysis.
recently i used pycortex to visualize HCP fmri data,HCP data are all on MNI space ,if you have unic xfm trasforme matrix for each subject to MNI space you can do this with just one set of surface gifti files.
i used cortex.xfm.Transform to obtain xfm matrix.
connectome workbench in also a very nice program for visualization.
this is just my experience, hope it helps.