External Email - Use Caution Bruce,
Oh okay I understand now. This has been very enlightening! So, you think if I let it keep running it will eventually correct the defects? And then I just need to double check the result to make sure it corrected them properly? When I got the overlay to work, I could see two big defects on the left hemisphere (30 and 41) so I guess it'll probably get stuck again on 40. Also, is there anything I can do to make it faster? 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 11:21 AM To: Freesurfer support list Subject: Re: [Freesurfer] CORRECTING DEFECT CAUTION: External yes, because that is the total # of defects. The 29th or 30th isn't the last one, just what it got stuck on. The #30 should look much bigger though (you'll need to change the overlay thresholds) On Fri, 9 Aug 2019, Balken, Brendan wrote: > 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 > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
