If you try with the beta version of FreeSurfer the mris_convert command may take care of what Donna was concerned about automatically or with an optional flag. That said, I asked you multiple times to provide the exact commands you were running and any error messages and you have not done that. It is hard to provide support without knowing those kind of details.
Peace, Matt. On 1/15/17, 1:06 PM, "[email protected] on behalf of Marta Moreno" <[email protected] on behalf of [email protected]> wrote: >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 Freesurfer¹s origin and your >>orig.mgz volume¹s origin. See this script: >> >> >>https://github.com/Washington-University/Pipelines/blob/7cc0bf1863cbc8a1a >>7ab9c6dd48a25de9be9bae7/PostFreeSurfer/scripts/FreeSurfer2CaretConvertAnd >>RegisterNonlinear.sh >> >> Search for c_ras.mat. This applies to surfaces in subject¹s volume >>space. >> >> If you map MNI FCmaps onto MNI surfaces, I¹d 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 >>won¹t 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 ³How do I map data between >>>FreeSurfer and HCP?², 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 ________________________________ 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
