I would try running with a different random seed and see if this fixes this issue.
Peace, Matt. From: <[email protected]<mailto:[email protected]>> on behalf of Antonin Skoch <[email protected]<mailto:[email protected]>> Date: Tuesday, November 8, 2016 at 5:19 PM To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: [HCP-Users] Pial surface misplacement Dear experts, I am checking quality of the pial and white surfaces generated by HCP pipeline in our data (with acquisition parameters set according to the HCP recommendations). I found that in some spots the pial surface does not seem to reasonably follow the underlying anatomy - it cut too much of gray matter and reaches almost to the white surface. I tracked the problem to the step in FreeSurferHiResWhite.sh where the file ?h.preT2.pass2 is generated (see the attached screenshot, blue surface is the pial.postT2.pass1, yellow surface is pial.preT2.pass2). Could you please comment on where could be the problem and how to face it? I suspect that this kind of error could have profound effect on the results. My second inquiry is, are the source codes of mris_make_surfaces of HCP version of FreeSurfer available? Or, how is the difference in code between standard 5.3.0 and HCP version? Regards, Antonin Skoch _______________________________________________ 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
