Re: [Freesurfer] recon-all segmentation error
does it segment the cerebellum ok? If so, it should be removed during recon-all On Fri, 3 Jun 2016, Jaiashre Sridhar wrote: Bruce, The aseg looks fine to me. Is there anything in specific that I should be looking for in aseg? Thanks, Jaiashre. ___ 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.
Re: [Freesurfer] recon-all segmentation error
Bruce, The aseg looks fine to me. Is there anything in specific that I should be looking for in aseg? Thanks, Jaiashre. ___ 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.
Re: [Freesurfer] recon-all segmentation error
hmmm, that suggests that the aseg failed badly. What does it look like? cheers Bruce On Fri, 3 Jun 2016, Jaiashre Sridhar wrote: Bruce, The lh.inflated.nofix shows the brainstem and cerebellum are attached to the cortical surface. Also, the ventricles are not filled in the filled.mgz. Could you please tell me how to fix this manually? Thanks, Jaiashre. ___ 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.
Re: [Freesurfer] recon-all segmentation error
Bruce, The lh.inflated.nofix shows the brainstem and cerebellum are attached to the cortical surface. Also, the ventricles are not filled in the filled.mgz. Could you please tell me how to fix this manually? Thanks, Jaiashre. ___ 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.
Re: [Freesurfer] recon-all segmentation error
Hi Jaiashre. looks like you created a huge topological defect with your edits. Check out the ?h.orig.nofix and ?h.inflated.nofix to see what happened. cheers Bruce On Wed, 27 Jan 2016, Jaiashre Sridhar wrote: Hello, We made changes to the aseg.mgz in the caudate, nucleus accumbens and ventricular region using Freeview. We are interested in getting the caudate volume. We used the following recon options in FreeSurfer v5.1.0: -autorecon2 –noaseg –autorecon3 Out of the 60 subjects that we ran, 4 exited with errors. I have provided the recon-all.log files. (1) Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 11 iterations mhtVoxelList_Add(204, 160, 213, 229294): complete list too big! .. (2) CORRECTING DEFECT 6 (vertices=43037, convex hull=2066) Segmentation fault (3) mri_fill: could not find pons find_cutting_plane:seed point not in structure! Searching neighborhood.. (4) CORRECTING DEFECT 0 (vertices=96569, convex hull=3716) Excessive topologic defect encountered: could not allocate 980957071 edges for retessellation Cannot allocate memory Any help is greatly appreciated! Thanks, Jaiashre. ___ 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.
