Dear Mingrui,

I’ve been trying to plot simultaneously a surface (lh.pial and rh.pial from FreeSurfer after merging them with the BrainNet tool) and a volume (the aparc+aseg VOI map, converted to a .nii file with mri_convert from FreeSurfer). Although I got no errors in the process, the pial surface and the VOIS are clearly misaligned, and the VOI map lies far away from the surface.

I read in a similar help topic that you recommended to comment a couple of lines in the BrainNet.m file to solve this problem. However, in the version I got, these lines are already commented and still have the same issue. Any help would be highly appreciated.

Dear Alexis, 

Could you please upload your files that I can have a check? I guess the surface and the volume are not in a same space.

Originally posted by Mingrui Xia:
Thanks for your quick reply. Attached are both pial surfaces (lh.pial and rh.pial) as provided by FreeSurfer, the merged surface (merged.nv) with the BrainNet tool, and the aparc+aseg.nii VOI map, obtained with FreeSurfer after converting it to .nii with FreeSurfer's mri_convert. I also attached a picture of the result of plotting a couple of VOIs and the surface. As can be seen, they are not aligned at all.

According to FreeSurfer documentation, pial surfaces and VOI maps are in the same space, .i.e., the so-called "Anatomical Space" of FreeSurfer. Thus, the problem might be the way that BrainNet handles the .pial files...

Dear Alexis,

I've checked your files. The X, Y, Z ranges for lh.pial and rh.pial are [-68.6418, 1.7941], [-94.3788, 55.5636], [-58.9766, 64.7290] and [-5.0226, 67.0435], [-95.0301, 53.5139], [-56.5119, 65.2336], respectively. This was loaded by the function read_surf.m provided by FreeSurfer. The XYZ space loaded by spm_vol.m and spm_read_vols.m in SPM are  [83.0915, 338.0915], [137.6303, 392.6303], [425.8168, 680.8168]. That's why they mismatched. I suggest to check if the VOI file shares space information with other anatomical images (e.g., original T1?).

Best,
Mingrui
Originally posted by Alexis Moscoso:

That was the problem. For some reason, Freesurfer VOIs were not centered where they should. After recentering and use Old Normalise from SPM to align with ch2 template I could use the smoothed_ch2 surface to cover my VOIs. Thanks for your help!
Originally posted by Mingrui Xia: