Exporting surface, not aligned with MRI in FreeView

edelaire · July 11, 2023, 5:23pm

Hello,
I was trying to export the cortical surface from Brainstorm and the associated MRI to visualize them in FreeView, but it seems the surfaces don't align well with the MRI (although they are aligned in Brainstorm).

To replicate, create a subject using the template ICBM and export the MRI as nii and the surface as .fs. and open them in FreeView. Note the issue seems to also be present if we export as .gii

it seems that the surface is rotated.

edit: if in Freeview, we first load the surface and then the MRI the co-registration seems better but still not perfect so I am not sure what the issue could be or if it is linked to brainstorm or FreeView (note that is no issue when loading directly surface/mri from the free surfer database)

Edouard

tmedani · July 13, 2023, 1:52am

Hi @edelaire
I have no experience using FreeView, but I guess some fields in the data (Transformation matrixes/headers, variables names ...) that are exported from Brainstorm are invisible or can't be read from FreeView.

It needs further investigation, and it may take some time from our side to get to this issue.

this is a good path to investigate, so we can compare the data structure in both files and check what are the differences.