Re: [Freesurfer] FS6 recon-all hangs at mris_fix_topology
Hi Bruce, Thanks, it does look like there is some skull included in the brainmask.mgz and wm.mgz in many locations (very noisy scan). I'll edit those out and give it another try. 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, January 24, 2017 9:58 AM To: Freesurfer support list Subject: Re: [Freesurfer] FS6 recon-all hangs at mris_fix_topology Hi Matt looks like you ahve a pretty big (almost 18K vertices) defect. It will eventually fix it, but possibly not in the correct way. You can load the lh.inflated.nofix in freeview and theoverlay lh.defect_labels to see what's going on (this is the first defect). It may be that some of the skull was left around or the cerebellum or something, in which case you'll want to manually correct the wm.mgz to remove the non-brain tissue cheers Bruce On Tue, 24 Jan 2017, Hibert, Matthew Louis wrote: > Hi Freesurfer Devs, > I'm trying to re-process a subject who had a right temporal lobectomy using > FS6 but the recon hangs at the mris_fix_topology step, saying "XL defect > detected...". It continues to use a CPU for several days if allowed, but > does not actually progress from that point. This scan was able to be > processed in both stable 4 and stable 5.3. I've attached the recon-all log > from the recon using the Martinos installation of "stable6". Any > suggestions? > > Thanks, > Matt > > ___ 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.
Re: [Freesurfer] FS6 recon-all hangs at mris_fix_topology
Hi Matt you only need to edit them if the lh.orig.nofix surface includes them. Otherwise they are fine. The first defect will be near the back of the brain cheers Bruce On Tue, 24 Jan 2017, Hibert, Matthew Louis wrote: > Hi Bruce, > Thanks, it does look like there is some skull included in the brainmask.mgz > and wm.mgz in many locations (very noisy scan). I'll edit those out and give > it another try. > > 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, January 24, 2017 9:58 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] FS6 recon-all hangs at mris_fix_topology > > Hi Matt > looks like you ahve a pretty big (almost 18K vertices) defect. It will > eventually fix it, but possibly not in the correct way. You can load the > lh.inflated.nofix in freeview and theoverlay lh.defect_labels to see > what's going on (this is the first defect). It may be that some of the > skull was left around or the cerebellum or something, in which case you'll > want to manually correct the wm.mgz to remove the non-brain tissue > > cheers > Bruce > > > On Tue, 24 Jan 2017, Hibert, > Matthew Louis wrote: > >> Hi Freesurfer Devs, >> I'm trying to re-process a subject who had a right temporal lobectomy using >> FS6 but the recon hangs at the mris_fix_topology step, saying "XL defect >> detected...". It continues to use a CPU for several days if allowed, but >> does not actually progress from that point. This scan was able to be >> processed in both stable 4 and stable 5.3. I've attached the recon-all log >> from the recon using the Martinos installation of "stable6". Any >> suggestions? >> >> 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 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.
Re: [Freesurfer] FS6 recon-all hangs at mris_fix_topology
Hi Matt looks like you ahve a pretty big (almost 18K vertices) defect. It will eventually fix it, but possibly not in the correct way. You can load the lh.inflated.nofix in freeview and theoverlay lh.defect_labels to see what's going on (this is the first defect). It may be that some of the skull was left around or the cerebellum or something, in which case you'll want to manually correct the wm.mgz to remove the non-brain tissue cheers Bruce On Tue, 24 Jan 2017, Hibert, Matthew Louis wrote: Hi Freesurfer Devs, I'm trying to re-process a subject who had a right temporal lobectomy using FS6 but the recon hangs at the mris_fix_topology step, saying "XL defect detected...". It continues to use a CPU for several days if allowed, but does not actually progress from that point. This scan was able to be processed in both stable 4 and stable 5.3. I've attached the recon-all log from the recon using the Martinos installation of "stable6". Any suggestions? Thanks, Matt ___ 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.
