External Email - Use Caution Bruce,
I just imported lh.defect_labels as an overlay over the lh.inflated.nofix but the values aren't 1-30 they're 0 - 160 roughly. I'm not sure why... Thanks! -----Original Message----- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Friday, August 9, 2019 11:00 AM To: Freesurfer support list Subject: Re: [Freesurfer] CORRECTING DEFECT CAUTION: External they are an overlay not a surface. Load the surface first then load them as an overlay on top of it (e.g. the lh.inflated.nofix) On Fri, 9 Aug 2019, Balken, Brendan wrote: > External Email - Use Caution > > Bruce, > > Thanks so much for the quick response! I don't know how to load the defect > labels. When I try to load them as a surface, I get an error. I'm doing this > in freeview gui. Also, I checked the cerebellum and it's not attached. > > Thanks, > Brendan > > -----Original Message----- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce > Fischl > Sent: Friday, August 9, 2019 10:27 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] CORRECTING DEFECT > > CAUTION: External > > Hi Brendan > > the time to correct goes with the square of the size of the defect (actually > the convex hull of the defect) so it can take a very long time for big ones. > More importantly, if the defect is that large it may not be corrected in the > anatomically desired manner. You should take a look at it and see what is > causing it. Is skull left over? Cerebellum attached? > Hemispheres connected? Usually the big ones are due to something dramatic. > Look at the ?h.orig.nofix and the ?h.inflated.nofix. YOu can load the > ?h.defect_labels on top of the surfaces and brain.mgz and the wm.mgz to see > which one is 29 (note that they defect_labels file is probably 1-based so you > would need to look for 30 in it). > > If you can't sort it out gzip and tar your subject and put it on our > ftp site and we will take a look for you cheers Bruce > > On Fri, 9 Aug 2019, Balken, Brendan wrote: > >> >> External Email - Use Caution >> >> Hello! >> >> >> >> So I am attempting to use freesurfer’s recon-all script but for one >> of our subjects I keep getting stuck at this point: “CORRECTING >> DEFECT 29 (vertices=19321, convex hull=4029, v0=32423) XL defect >> detected...” It has already corrected 28 defects, but they were much >> smaller. It has been running for about 48 hours on a very powerful >> machine and I’m wondering how long I should wait. Will it eventually >> move on? If no, what is my contingency plan for processing this? I’m >> using the output anatomy folder in brainstorm for source analysis. >> Any guidance or information would be greatly appreciated. >> >> >> >> Thanks a million! >> >> Brendan >> >> >> >> >> >> Here’s what the lh and rh.inflated.nofix look like (is that the defect?): >> >> >> >> [IMAGE] >> >> >> > > _______________________________________________ > 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
