thanks Dr. Fischl,

Would there be a reason as to why recon-all crashed when doing the conformation then? I got the following error in my terminal:

Original Data has (0.5, 0.5, 0.5) mm size and (394, 466, 378) voxels.
Data is conformed to 1 mm size and 256 voxels for all directions
changing data type from short to uchar (noscale = 0)...
MRIchangeType: Building histogram
Reslicing using trilinear interpolation
writing to /data-01/trisanna/freesurfer/MNI_average_2009b_asymm/mri/orig.mgz...

mri_add_xform_to_header -c /data-01/trisanna/freesurfer/MNI_average_2009b_asymm/mri/transforms/talairach.xfm /data-01/trisanna/freesurfer/MNI_average_2009b_asymm/mri/orig.mgz /data-01/trisanna/freesurfer/MNI_average_2009b_asymm/mri/orig.mgz

INFO: extension is mgz
#--------------------------------------------
#@# Talairach Tue May 24 19:10:10 EDT 2016
/data-01/trisanna/freesurfer/MNI_average_2009b_asymm/mri

mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz

recon-all -s MNI_average_2009b_asymm exited with ERRORS at Tue May 24 19:11:34 EDT 2016

Ph.D. Candidate

McGill University

Integrated Program in Neuroscience

Psychology

On Wed, May 25, 2016 at 6:49 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

Hi Trisanna

you can use the -cm flag, but typically what we do is let recon-all
"conform" the data to 1mm, then do a post-hoc surface deformation with
the original highres data using mris_make_surfaces

cheers
Bruce
On Wed, 25 May 2016, Trisanna Sprung-Much wrote:

> Hi there
>
> My initial email didn't seem to have sent and so I am re-sending it:
>
> I would like to know if it is possible to create surfaces from a scan that
> is 0.5mm isotropic. I tried to run recon-all on our MNI 2009b atlas which is
> 0.5mm cubed and it crashed quite quickly afterwards. I wonder if this has to
> do with the fact that Freesurfer tried to conform it to 1mm isotropic?
>
> When I ran recon-all on the 1mm atlas it created some nice surfaces.
>
> Let me know if you would like the .log as I cannot seem to make much sense
> of it.
>
> best wishes
>
> Trisanna
> --
> Ph.D. CandidateMcGill University
> Integrated Program in Neuroscience
> Psychology
>
>
>
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