Re: [HCP-Users] Pial surface

[Erin Reid]

Hi Mahmoud, The pial (blue) surface line is intended to hit the very outer edge of the pial surface.  There are plenty of times that the image is not clear enough for FreeSurfer to do a "perfect" job so some dura (or blood vessels) can sometimes be included in the pial surface outline.  For our purposes, we decided not to fix these when they were minor instances (i.e. not causing significant surface errors).  If you are wishing to tweak the results, hopefully Mike Harms can give you some pointers on doing so. Erin Reid On 12/28/15 10:04 AM, Mahmoud wrote: Hello All, I've applied HCP pipeline scripts to our structural data and it looks like everything goes well to the end of PostFreeSurferPipelline. Opening the fs_LR.wb.spec file for the low-resolution mesh, it is obvious that the pial surface line (the blue line) hits the dura or is at the very outer edge of the pial surface. I was wondering which parameters and where I should tweak to get a better result. Thank you! Mahmoud _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users