Hi Falk, I used the command and got the following error: Command: ris_topo_fixer -mgz -warning -seed 1234 ICBM lh mris_topo_fixer -mgz -warning -seed 1234 ICBM lh INFO: assuming .mgz format setting seed for random number genererator to 1234 reading input surface /home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mni_icbm152_nlin_sym_09b/ICBM/surf/lh.orig... mrisFindNeighbors: /home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mni_icbm152_nlin_sym_09b/ICBM/surf/lh.orig: face[46196].v[0] = 24215, but face 46196 not in vertex 24215 face list
mris_topo_fixer -mgz -warning -seed 1234 ICBM rh INFO: assuming .mgz format setting seed for random number genererator to 1234 reading input surface /home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mni_icbm152_nlin_sym_09b/ICBM/surf/rh.orig... mrisFindNeighbors: /home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mni_icbm152_nlin_sym_09b/ICBM/surf/rh.orig: face[35822].v[2] = 18903, but face 35822 not in vertex 18903 face list Any suggestions would be appreciated. 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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