yes, and autorecon3 On Fri, 26 May 2017, Hibert, Matthew Louis wrote: > Thanks Bruce. After I remove the problem voxels in wm.mgz, do I then re-run > the recon from autorecon2-wm? > > Thanks, > Matt > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Friday, May 26, 2017 1:40 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] 7T recon > > Hi Matt > > yes, that means there was a topological defect that was incorrectly > fixed. If you load the wm.mgz over the lh.orig.nofix, then in the > orig.nofix load the file defect_labels as an overlay and change the overlay > settings to that the min is 1 and click the "use overlay color" button it > will show you the regions of the surface that are defective. You will then > need to edit the wm.mgz to remove the handle/hole that is the defect. > > cheers > Bruce > > > On Fri, 26 May 2017, Hibert, Matthew Louis wrote: > >> Hi All, >> I reconstructed 20 subjects with a 750um isotropic MPRAGE collected at 7T >> and while most look good, 4 of the subjects have a similar section of the >> left STG removed from the final surfaces (picture attached). In all 4 >> subjects the entire left STG is included in the wm.mgz and lh.orig.nofix >> (red), but a portion has been removed in lh.orig (yellow), so the problem >> seems to occur in the -fix stage of autorecon2. >> >> How can I go about correcting this issue? >> >> Thanks, >> Matt >> >> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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