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
