Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure (mris_euler_number) using high res (0.5mm isotropic) T1 image

Hi Falk

I don't think you need to rerun the qsphere. I'm pretty sure this is a bug in mris_fix_topology for giant defects, but haven't finished tracking it down yet

cheers Bruce

On Tue, 1 Dec 2015, Falk Lüsebrink wrote:

Hi Ajay,

you should

cp ?h.orig.nofix ?h.orig

cp ?h.inflated.nofix ?h.inflated

with ? being l or r depending your hemisphere. After the fixing stage the surfaces got damaged somehow, therefore you have to recreate it them. I’m not entirely sure about the qsphere. Probably you have to run the -qsphere stage again also.

Best,

Falk

Von: Ajay Kurani [mailto:dr.ajay.kurani@gmail.com] Gesendet: Montag, 30. November 2015 21:50 An: Falk Lüsebrink Cc: Freesurfer support list; Bruce Fischl Betreff: Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure (mris_euler_number) using high res (0.5mm isotropic) T1 image

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