You should run the specific command that generates the .rot. file in PostFreeSurfer to get that file. Starting with FreeSurfer for MSMAll is definitely not recommended as that will make the problem harder for MSMAll (having to try to undo the bad FreeSurfer distortions), and it might be better to rerun PostFreeSurfer before using MSMAll.
Peace, Matt. From: <[email protected]<mailto:[email protected]>> on behalf of Timothy Hendrickson <[email protected]<mailto:[email protected]>> Date: Tuesday, July 10, 2018 at 10:24 AM To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: [HCP-Users] Core Dump ${MSMBINDIR}/msm Hello, When I run msm within MSMAll I get a core dump because the --inmesh file could not be found: ${NativeFolder}/${Subject}.${Hemisphere}.sphere.rot.native.surf.gii. I see that the file is generated within the PostFreeSurfer pipeline if the MSMSulc registration is specified. I've already run minimal preprocessing on this study with FS as registration name. While I will ultimately switch all of my processing to MSMSulc I would like to keep the preprocessing I have done with FS there. What file should I use then for inmesh? -Tim Timothy Hendrickson Neuroimaging Analyst/Staff Scientist University of Minnesota Informatics Institute University of Minnesota Bioinformatics M.S. Candidate Office: 612-624-0783 Mobile: 507-259-3434 (texts okay) _______________________________________________ HCP-Users mailing list [email protected]<mailto:[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
