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Hi Greve, Yes that is the inflated surface, lets go by parts, so basically the orig surfaces are actually fine as you can see in the first image here:
As for the white surfaces, they haven't been generated because as i explained freesurfer didn't finished because my job run out of cpu time. I think the problem starts in the inflated.nofixes surface, I am sending you some screenshots of them, but my impression is that the image is not properly aligned to them:
I also checked the skull stripping and is fine, I am writing because I followed the https://fscph.nru.dk/slides/Allison/freesurfer.failure_modes.pdf slides and this kind of error is definitely not here. As you can see in the image there is something terribly wrong with inflated.nofix images, basically right and left side are overlapping. Do you know what could be originating this?
Thanks for the help, Vicente Ferrer Predoctoral Researcher BCBL www.bcbl.eu
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From: "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu To: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, November 12, 2019 4:46:49 PM Subject: Re: [Freesurfer] Recon all hard failure,
And before that you should check the orig and white surfaces
On 11/12/2019 9:37 AM, Bruce Fischl wrote:
Hi Vicente
I'm not sure what the images are showing - maybe the inflated surface? That isn't useful to look at in the volume. You should check the inflated.nofix surface and see if something big is wrong (cerebellum or skull attached, that kind of thing). There is a tutorial on our wiki for correcting this kind of defect
cheers Bruce
On Tue, 12 Nov 2019, Vicente Ferrer wrote:
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Hello,
I was runnning reconall in one of my images and it got stucked fixing surface defects, since i run it on a cluster it stopped when it runned out from cpu time. As you will see in the log the command started in SUNday 16 14:59:32 CEST 2019 and ended in Mon Jun 17 05:10:16 CEST 2019 which is more than usual for a recon-all duration. I have checked some of the previous images and there is clearly an alignment problem as you can check in this image:
Vicente Ferrer Predoctoral Researcher BCBL www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
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