Dear Brainstorm users,
I have a dataset with warped anatomical pial surfaces obtained by the usual Brainstorm procedure.
In order to run a MVPA analysis in MATLAB I need to export them in FreeSurfer format. I tried selecting the surface and saving as a *.fs file but it gives me a single mesh (both hemispheres) while I need two separated left/right mesh like in a standard FreeSurfer output.
Do you have any hint on how to do it?
Many thanks in advance !
D.
Hello
Indeed, the export function to the FreeSurfer format does not separate the two hemispheres. This output is not designed to go back to the FreeSurfer database, and we thought it was going to be used so little, we never put a lot of work into it.
One thing you could try would be to open the cortex (high-resolution probably?), in the Scout tab select the atlas "Structures", select one hemisphere (left or right) and use menu Scout > Edit surface > Keep only selected scout. This would create a new "cortex_...V | keep" file with just one hemisphere. Finally export this one as a FreeSurfer surface. Repeat with the other hemisphere.
I'm not sure this would give what you need, and it might not fall back into the initial FreeSurfer space (ie. the surfaces might not be aligned on the T1.mgz volume).
Does this help?
Thanks Francois,
this was indeed very helpful since, in principle, we don't need in MVPA the alignement with the original T1 from he FreeSurfer database.
Are the coordinates exported in this way to the *.fs files in MNI?
Many thanks !
D.
The exported surfaces are in the same space as what they appear in your database, there are no additional transformations applied.
If you are using surfaces extract from the subject's MRI (using FreeSurfer, BrainSuite or BrainVISA) or if you have warped the template surfaces (ICBM152) using digitized head points (https://neuroimage.usc.edu/brainstorm/Tutorials/TutWarping), then the surfaces are in subject space.
If you are using directly the ICBM152 template, then the surfaces are in MNI space.