> On 24 Aug 2015, at 22:12, John Baublitz <jb...@bu.edu> wrote:
>
> I am trying to export functional data from PyMVPA. Our lab is specifically
> trying to load functional data from the analysis (a list of vertices and a
> value associated with each vertex from the analysis) and visualize it in
> FreeSurfer. As I understand it, I have been saving it as functional data
> (using map2gifti) based on the update to PyMVPA that you committed.
> Unfortunately there seems to be an issue where FreeSurfer will not load an
> overlay with an extension .gii. I am happy to email FreeSurfer if this is
> more of a FreeSurfer issue but it seems that the .gii file output by PyMVPA
> does not really work with any FreeSurfer utils, not just the visualization as
> I mentioned with mris_convert. I am still unsure of where this issue is
> coming from: FreeSurfer or PyMVPA.
It seems it is due to a combination of the two:
- FreeSurfer seems to require the presence of anatomical data (vertices and
faces) in a GIFTI file, even for functional data.
- The recent updates in PyMVPA could result in writing GIFTI-incompatible data,
in particular when data was provided as float64 or int64 data. GIFTI only
supports 8 and 32 bit data.
I've added support to the map2gifti function for a "surface" argument, which
takes a anatomical Surface object (from mvpa2.support.nibabel.surf) or a
filename of an anatomical surface. Also, data is casted to 32 bit
representations. Storing GIFTI overlay data together with the anatomical data
seems to make mris_convert happy. This is currently submitted in a PR [1].
For example, if ds is a PyMVPA dataset, you can do:
from mvpa2.suite import *
anat_surface=surf.from_any('pial.gii')
map2gifti(ds, filename='data_for_mris_convert.gii', surface=anat_surface)
and then
mris_convert data_for_mris_convert.gii data.asc
Can you see if this PR fixes the GIFTI issues for you?
[1] https://github.com/PyMVPA/PyMVPA/pull/357
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