What version of Freesurfer are you using? There was a specific one for the pipelines, and the version did affect results in the medial temporal especially, but also the insula.
On Dec 28, 2015, at 12:56 PM, Mahmoud <zeydab...@gmail.com> wrote: > Hello Erin, > > Thank you for your response. I was hoping there are some parameters to tweak > so I can compare the results and see which one makes more sense. Currently, > it looks to me that the occipital and temporal lobe surfaces are not accurate > enough. This made the mylin maps to show less amount of myelins, colored > mostly green and yellow, while I was expecting more red. > > Thank you, > Mahmoud > > On Mon, Dec 28, 2015 at 1:17 PM, Erin Reid <e...@brainvis.wustl.edu> wrote: > 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 > > > _______________________________________________ > 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
