Thank you, Dona. I tried that too but I am getting similar pictures. Any other recommendation? I got very nice results from analyses and need nice pictures.
Thanks, -L > On Jan 15, 2017, at 10:40 AM, Dierker, Donna <[email protected]> wrote: > > 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
