Thank you again for your reply. For editing aseg.mgz, as mentioned in https://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide/TkMeditWorkingWithData/FreeviewSegmentations
it does suggest using -autorecon2-noaseg, but from what I can see this does not update the aparc+aseg.mgz and associated .stats etc is that correct? Doesn't this command (as does -autorecon3) also re-create surfaces that would need to be re-checked and re-edited if needed? Also, I think FS5.1 does not have the -autorecon2-noaseg flag. As an alternative, with completed wm/pial boundaries could we run recon-all -surfsegedit, then we would edit aseg as needed and then: recon-all -aparc2aseg -segstats -wmparc This will not change any surfaces but would update aseg.stats aparc.a2009s+aseg.mgz wmparc.mgz wmparc.stats etc P ---- On Mon, 20 Apr 2015 13:42:49 -0700 Martin Reuter<mreu...@nmr.mgh.harvard.edu> wrote ---- Hi so take a look at https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData where the entry points are described ( for brainmask and finalsurfs -autorecon-pial should be OK, for aseg it says to use -autorecon2-noaseg ) Also this page https://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFlags has details on the steps. Best, Martin On 04/20/2015 03:21 PM, Martin Reuter wrote: 553551cf.30...@nmr.mgh.harvard.edu" type="cite"> Hi P, usually edits to surfaces should not be required in the long. The surfaces there get initialized from the base, so you need to make sure the base surface is as accurate as possible. Several edits also get transferred automatically from the cross sectional runs. See this http://freesurfer.net/fswiki/LongitudinalEdits for a description of the different edits, and where they should be done. About where to restart after making the edits, everything should be done the same way as in the regular (cross sectional) processing. So you specifically ask about: - brainmask edits - brainfinalsurf edits - and manual aseg edits. I just looked at the description of those regular edits http://freesurfer.net/fswiki/Edits but sadly there it does not say where to start re-run either. I'll try to find out and update that soon. I hope someone with editing experience can chime in and tell us. (I changed the subject, so that it get's read). Cheers, Martin On 04/20/2015 09:44 AM, Bruce Fischl wrote: ne.lrh.2.11.1504200944020.9...@gate.nmr.mgh.harvard.edu" type="cite">I'll leave the first question for Martin but it looks right to me (except for the typo in what should be "-autorecon3"). For the second one I think you want to rerun the mri_segstats and mris_anatomical_stats commands, which should be done by autorecon3 cheers Bruce On Mon, 20 Apr 2015, prasser wrote: Dear All, I wanted to check that corrections to a Long pial surface through edits to brainmask.mgz and brain.finalsurfs.manedit.mgz are followed by the command: recon-all -long tpN1 templateID -autorecon2-pial -autorecom3 Is this correct? Also, after editing the Long aseg.mgz to correct the volume of structures what command should be run to have these edits update the dependent files? Thanks, P _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu _______________________________________________ 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.
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