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
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
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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@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
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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@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
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