Hi Leah, I wonder if you need to apply an affine transform to your white/pial surfaces to adjust for the offset between Freesurfer’s origin and your orig.mgz volume’s origin. See this script:
https://github.com/Washington-University/Pipelines/blob/7cc0bf1863cbc8a1a7ab9c6dd48a25de9be9bae7/PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear.sh Search for c_ras.mat. This applies to surfaces in subject’s volume space. If you map MNI FCmaps onto MNI surfaces, I’d expect better alignment, but if you use a nonlinear method to get FCmaps on MNI, but just apply the talairach.xfm to the surfaces (linear/affine), then that alignment won’t be as good as if you used the same method for both. Donna > On Jan 15, 2017, at 1:40 AM, Leah Moreno <[email protected]> wrote: > > Dear experts, > > I have individual FCmaps in mni & subject volume space (not using HCP or > FreeSurfer) and individual surface data from FreeSurfer. I want to map data > from individual volumes to individual surfaces to then average across > subjects on the surface and visualize with workbench. But the volume data is > not being well mapped to the surface, please see attachment. > > I have also tried section B. of document “How do I map data between > FreeSurfer and HCP?”, but either with or without resampling the output does > not look ok. > > Any help, please? > > Thank you, > > -L > > <image001.png> > > > > > > > > > > > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > <image001.png> ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
