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
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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