That is the right one, as far as I know. Matt Glasser or Michael Harms may know tweakable parameters, but I do not, unfortunately. Not sure how accessible they are this week (holiday break).
I wonder if it might be worth posing your question to the Freesurfer list, as it is really a Freesurfer segmentation issue, as I understand it. They might want you to try a newer version, though, and I'm not sure what downstream effects this will have on the pipeline. On Dec 28, 2015, at 1:46 PM, Mahmoud <[email protected]> wrote: > From the output log: > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-HCP > > On Mon, Dec 28, 2015 at 2:29 PM, Donna Dierker <[email protected]> > wrote: > 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 <[email protected]> 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 <[email protected]> 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 > >> [email protected] > >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users > >> > > > > _______________________________________________ > > HCP-Users mailing list > > [email protected] > > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > > > > _______________________________________________ > > HCP-Users mailing list > > [email protected] > > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
