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