Re: [HCP-Users] Freesurfer pipeline and subject's native surfaces

[Harms, Michael]

Hi, Are you comparing the FS output in '$subject/T1w/$subject/surf/{lh,rh}.white' to '$subject/T1w/Native/$subject.{L,R}.white.native.surf.gii? Because those should indeed have the same number of vertices and faces for a given hemisphere. Rather than using 'mris_convert', what happens if you just use 'mris_info' directly on the lh.white file, and 'wb_command -file-information' on the L.white.native.surf.gii file? cheers, -MH --  Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO  63110 Email: mha...@wustl.edu From: Tara Ganepola <tganep...@gmail.com> Date: Thursday, June 4, 2015 11:07 AM To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: [HCP-Users] Freesurfer pipeline and subject's native surfaces Hello,  My question is related to the FreeSurfer pipeline scripts and the contents of the 'subject/T1w/Native/' directories. After running the FreeSurferPipelineBatch.sh locally should I expect the surfaces to be identical to those found in 'subject/T1w/Native/' or is there an additional step of processing between these?  I have done this for a few subjects and noticed that the vertex count is different. For example for subject 100307 the file 100307.R.white.native.surf.gii has 128346 vertices and the output of the FreeSurfer pipeline, rh.white has 128900. (the vertex counts were determined by converting to ascii format using mris_convert).  Ultimately, I am aiming to sample the diffusion weighted data at different cortical depths with an in house script that required freesurfer's binary surface format. I would like the best possible surfaces for subjects in their native space, the quickest method would be to convert the provided gifti files back, but as the files seem to have different vertex counts I was unsure whether they are equivalent or if they have been through some transformation?  Many thanks Tara _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org 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 HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users