Hi Matt can you tar and gzip your subject and upload it to our ftp site? Bruce On Wed, 7 Jun 2017, Hibert, Matthew Louis wrote:
> Hi Bruce, > I edited the wm.mgz with the recon-editing tool this time, removing the > problem areas near this defect (primarily lots of dura originally included), > and confirmed that my edits remained after re-processing. However, the left > STG is still being removed, images attached (red is the lh.orig.nofix with > lh.defect_labels overlayed, yellow is lh.white). The entire left STG is > still being marked as a defect despite my edits. Any suggestions? > > Thanks, > Matt > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Hibert, Matthew Louis > [mhib...@mgh.harvard.edu] > Sent: Tuesday, June 06, 2017 5:22 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] 7T recon > > Ah ok, thanks Bruce. > > 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: Tuesday, June 06, 2017 4:35 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] 7T recon > > Hi Matt > we keep track of edits by setting erased voxels to 1, not 0. If you do > the editing within freeview using the "recon edit" tool, this will happen > automatically > > cheers > Bruce > On Tue, 6 Jun 2017, Hibert, Matthew Louis wrote: > >> Hi Bruce, >> Thanks again for your help so far. I've tried removing the problem voxels >> from the wm.mgz (setting their value to 0), saving the wm.mgz, and then >> running "recon-all -autorecon2-wm -autorecon3 -hires -s $SUBJECT -xopts-use >> -openmp 2". However, the edits to the wm.mgz are not incorporated and the >> surfaces are not changed; when I open the wm.mgz again, the voxels I removed >> are now present again. What am I doing wrong? >> >> 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 1:57 PM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] 7T recon >> >> 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 >> >> _______________________________________________ >> 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 > > _______________________________________________ > 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 The information in this e-mail is intended only for the person to whom it is addressed. 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