[color=#000000]Hi Daniel,[/color]
[color=#000000]The mask.volume.brainmask.nii and mask.surface.brainmask.nii files are only used as potential analysis-masks (when selecting those in the Setup.Options tab) but are otherwise not used in the 3D ROI-to-ROI displays (they represent default analysis masks for voume- and surface- based analyses, respectively). If you want to modify the default 3D surfaces shown in the ROI-to-ROI 3d displays (or the surface- and volume- seed-to-voxel displays) you would typically need to replace the files named lh.* and rh.* in the conn/utils/surf directory (e.g. lh.white.surf, lh.pial.surf, etc.) with equivalent freesurfer files of your reference cat brain (these files are in the same format as those lh.white and lh.pial files directly generated by freesurfer when processing your structural volumes).[/color]
[color=#000000]Let me know if you run into any issues[/color]
Best
Alfonso
[color=#000000]
[/color][i]Originally posted by Daniel Stolzberg:[/i][quote]Hello CONN forum,
I have been trying to modify the default surface files (/conn/utils/surf/) to map ROI-to-ROI results onto a cat brain. We have a surface model made in FreeSurfer and I have been simply replacing the appropriate default *.surf files with the new ones. Results explorer correctly shows the cat brains around the Connectome Ring, however the 3D Display does not work. After some debugging, I think the issue is that I need to also change the mask.surface.brainmask.nii file; however, I have no idea what this file actually represents. I replaced the mask.volume.brainmask.nii file with the appropriate cat brain mask, but the mask.surface.brainmask.nii file is hard to decipher.
Anyone have experience with using custom surface files? Anyone have any idea what the mask.surface.brainmask.nii file contains?
While solving this part will get me a bit closer to a 3D display of the cat brain, does anyone have any further advice on some additional files I would need to replace?
Thank you in advance,
Dan[/quote]
[color=#000000]The mask.volume.brainmask.nii and mask.surface.brainmask.nii files are only used as potential analysis-masks (when selecting those in the Setup.Options tab) but are otherwise not used in the 3D ROI-to-ROI displays (they represent default analysis masks for voume- and surface- based analyses, respectively). If you want to modify the default 3D surfaces shown in the ROI-to-ROI 3d displays (or the surface- and volume- seed-to-voxel displays) you would typically need to replace the files named lh.* and rh.* in the conn/utils/surf directory (e.g. lh.white.surf, lh.pial.surf, etc.) with equivalent freesurfer files of your reference cat brain (these files are in the same format as those lh.white and lh.pial files directly generated by freesurfer when processing your structural volumes).[/color]
[color=#000000]Let me know if you run into any issues[/color]
Best
Alfonso
[color=#000000]
[/color][i]Originally posted by Daniel Stolzberg:[/i][quote]Hello CONN forum,
I have been trying to modify the default surface files (/conn/utils/surf/) to map ROI-to-ROI results onto a cat brain. We have a surface model made in FreeSurfer and I have been simply replacing the appropriate default *.surf files with the new ones. Results explorer correctly shows the cat brains around the Connectome Ring, however the 3D Display does not work. After some debugging, I think the issue is that I need to also change the mask.surface.brainmask.nii file; however, I have no idea what this file actually represents. I replaced the mask.volume.brainmask.nii file with the appropriate cat brain mask, but the mask.surface.brainmask.nii file is hard to decipher.
Anyone have experience with using custom surface files? Anyone have any idea what the mask.surface.brainmask.nii file contains?
While solving this part will get me a bit closer to a 3D display of the cat brain, does anyone have any further advice on some additional files I would need to replace?
Thank you in advance,
Dan[/quote]