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

Hi Ajay

if you can use our ftp or file drop, both linked at:

https://surfer.nmr.mgh.harvard.edu/fswiki

then I'll take a look. And yes, uploading the entire subject dir will make it easier.

cheers Bruce

On Mon, 30 Nov 2015, Ajay Kurani wrote:

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.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
  >
  >