Hi Rito the control points you have look like they are in voxels that contain some gray matter, which will probably make things worse. YOu need to identify why you are missing that part of the surface. Is the dark stuff there labeled as white? Maybe it's a topological defect that gets filled incorrectly?
cheers Bruce On Wed, 6 Jul 2016, Ritobrato Datta wrote: > Hi All, > > We have run recon-all on T1 FLASH images have identified regions where the > sulci were included inside the white matter boundary. We added controls > points around the sulci (please see attached pic) and reran recon-all as > follows > > recon-all -autorecon2-cp -autorecon3 -subjid <subject> > > but on a lot of instances, the specified control points were not incorporated > (please see attached image). How do we fix this, now that we have already run > the recon-all with -autorecon2-cp and the error persists ? > > Can someone please suggest ? > > Thank you, > > Rito and Jack > > _______________________________________________ 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.
