Hi Falk, Thank you very much for the suggestion! I will give it a try. Also Bruce I sent a separate email with a link to the original image for you to download. I can also move all of my processed files for that template there if you would like so you do not have to restart from scratch?
Thanks, Ajay On Mon, Nov 30, 2015 at 2:41 AM, Falk Lüsebrink <falk.luesebr...@ovgu.de> wrote: > Hi Ajay, > > I ran into the same error processing hires data a while ago using a > nightly build of centos 6 with the hires flag only. Disk space or alike > wasn't an issue. I ran mris_topo_fixer instead of mris_fix_topology to get > working surfaces. > > Best, > Falk > > -----Ursprüngliche Nachricht----- > Von: freesurfer-boun...@nmr.mgh.harvard.edu [mailto: > freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl > Gesendet: Sonntag, 29. November 2015 22:48 > An: Freesurfer support list > Betreff: Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure > (mris_euler_number) using high res (0.5mm isotropic) T1 image > > Hi Ajay > > are you sure you didn't run out of disk space? That error is a sanity > check on the surfaces that should never occur > > cheers > Bruce > On Sun, 29 Nov 2015, Ajay > Kurani wrote: > > > Hello Freesurfer experts, > > I am trying to run Freesurfer 6.0 beta (downloaded 10/15/15 > > version) with the -hires flag to process an MNI template image which > > is 0.5mm isotropic. Stage 1 ran well and on stage 2 there is an error > > during > > pocessing: > > > > Command run: > > recon-all -s ICBM -autorecon2 -openmp 8 -3T -hires -expert expert.opts > > > > I supplied a skull stripped brain which was nu corrected and so I used > > the T1.mgz and copied it to brainmask.mgz and nu.mgz in autorecon1 > > stage. I then ran autorecon2 and it was working well until I was at > > the -fix stage and ran into the following error: > > > > > > Error: > > mris_euler_number ./surf/lh.orig > > mrisFindNeighbors: ./surf/lh.orig: face[46196].v[0] = 24215, but face > > 46196 not in vertex 24215 face list > > > > > > > > I am not sure if this is due to the fact that we have a very high > > resolution image (template) and if there are any modifications needed > > aside from the hires flag. Are there any suggestions you have? > > > > Thanks, > > Ajay > > > > >
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