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.luesebrink@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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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
>
>