Hi Mark, I had a somewhat similar issue in the temporal lobe, which was due to the gray matter being darker than what FreeSurfer assumes. This caused the gray-pial boundary to be placed closer to the white surface than it should be.
For me the solution (suggested by Bruce) was to call mris_make_surfaces with special flags: mris_make_surfaces -max_gray_at_csf_border <inensity1> -max_csf <intensity2> where intesity1 and intensity2 are the maximally allowed image intensities for the gray and csf, set explicitly. It "guides" FreeSurfer to find the pial surface. Not sure if this will help in your case, but maybe worth a try if nothing else works. Natalia On Tue, 17 Feb 2015 11:03:24 -0600 Mark Fletcher <fletc...@illinois.edu> wrote: > Dear FreeSurfer Team, > > For some of my brains, I cannot seem to help FreeSurfer trace the pial > surface near the insula for some (but not all) of my subjects. I have > attached a powerpoint file with screenshots to this link for NMR users ( > http://gate.nmr.mgh.harvard.edu/filedrop2/?p=41pbame2sz8 ) > > Although only showing you one slice in this powerpoint, this problem > persists for about 13 more slices (in the axial view) > > I have tried adding control points near the grey/white matter boundary. > I have also tried edits to the white matter. Additionally, I have tried > “over tracing” the white matter near the un-traced region (this was a > suggestion I received from a staff member when I attended the “FreeSurfer > Workshop” in Boston). > > Do you have any other suggestions about how I can get this insula region > traced? Is their a way I can manually extend the pial surface itself to > the correct position? > > By the way, I am using the latest version of FreeSurfer (5.3.0) with a 3T > Siemens TRIO. > > > Thanks for your help. > > -Mark Fletcher _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
