Sorry for the delay. I have been traveling. I did not try to load them as both at the same time. I tried to load it as a surface and that threw an error in FreeSurfer (mris is NULL) and then I tried to load it as a volume and it didn't load either (no overlay data found in file). I am still struggling to figure out exactly how I should be loading this data. Is this a better question for FreeSurfer's mailing list? I'm not entirely sure as it seems possible that it could be either a format output issue (PyMVPA) or a FreeSurfer-specific issue.
On Thu, Jul 30, 2015 at 5:27 AM, Nick Oosterhof < n.n.ooster...@googlemail.com> wrote: > > > On 29 Jul 2015, at 20:57, John Baublitz <jb...@bu.edu> wrote: > > > > Thank you very much for the support. Unfortunately I have tried using > this GIFTI file that it outputs with FreeSurfer as an overlay and surface > > Both at the same time? > > > and it throws errors for all FreeSurfer utils and even AFNI utils. > FreeSurfer mris_convert outputs: > > > > mriseadGIFTIfile: mris is NULL! found when parsing file > f_mvpa_rh.func.gii > > > > This seems to indicate that it is not saving it as a surface file. > Likewise AFNI's gifti_tool outputs: > > > > ** failed to find coordinate/triangle structs > > > > How exactly is the data being stored in the GIFTI file? It seems that it > is not saving it as triangles and coordinates even based on the code you > linked to in the github commit given that the NIFTI intent codes are > neither NIFTI_INTENT_POINTSET nor NIFTI_INTENT_TRIANGLE by default. > > For your current purposes (visualizing surface-based data), consider there > are two types of "surface" GIFTI files: > > 1) "functional" node-data, where each node is associated with the same > number of values. Examples are time series data or statistical maps. > Typical extensions are .func.gii or .time.gii. > 2) "anatomical" surfaces, that have coordinates in 3D space (with > NIFTI_INTENT_POINTSET) and node indices in face information (with > NIFTI_INTENT_TRIANGLE). The typical extension is surf.gii. > > In PyMVPA: > (1) "functional" surface data is handled through mvpa2.datasets.gifti. > Data is stored in a Dataset instance. > (2) "anatomical" surfaces are handled through mvpa2.support.nibabel.surf > (for GIFTI, mvpa2.support.nibabel.surf_gifti). Vertex coordinates and face > indices are stored in a Surface instance (from mvpa2.support.nibabel.surf) > > (I'm aware that documentation about this distinction can be improved in > PyMVPA). > > > I've also run into a problem where the dataset that I've loaded has no > intent codes and unfortunately it appears that this means that the NIFTI > intent code is set to NIFTI_INTENT_NONE. > > Why is that a problem? What are you trying to achieve? If the dataset has > no intent, then NIFTI_INTENT_NONE seems valid to me, as the GIFTI standard > describes this as "Data intent not specified". > > > _______________________________________________ > Pkg-ExpPsy-PyMVPA mailing list > Pkg-ExpPsy-PyMVPA@lists.alioth.debian.org > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa >
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