Hi Antonin, where did you upload them to?
On 03/13/2017 05:51 PM, Antonin Skoch wrote: > Dear experts, > > in my longitudinal study with 2 timepoints I encountered issue with > aseg.presurf labeling and white/pial surface estimation of one subject > in region of occipital horns of lateral ventricle. The voxels in horns > are mislabeled as either white or gray matter or contain zero values. > I am still in the stage 1 of longitudinal stream, so this is classical > cross-sectional recon-all stream. > > I tried to reprocess this subject by using recon-all -s subj > -bigventricles -FLAIRpial (despite the fact that the subject does not > have generally enlarged ventricles I thought that this could help > nonlinear registration by mri_ca_register ). In case of timepoint 2 > this helped to correctly label left occipital horn and corrected error > with surfaces, but right occipital horn remained labeled as white matter. > > In contrast, in case of timepoint 1 the -bigventricles did not help to > label left occipital horn and additionally new massive error with > white surface placement appeared in the region of occipital horn of > left lateral ventricle. See the attached screenshots to ilustrate this > issue: > > tp1_nobigventricles_surface_OK > tp1_bigventricles_surface_error > tp2_nobigventricles_surface_error > tp2_bigventricles_surface_OK > > I have uploaded file > occipital_horn_ventricle_aseg_and_surf_error.tar.gz containing 4 > recons (timepoint 1 and 2 with and withoug -bigventricles) to your server. > > I suppose that the root of the problem is incorrect nonlinear > registration. Could you please advise how to diagnose and solve the error? > > I am using development version from beginning of february 2017. > > Regards, > > Antonin Skoch > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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.
