I see

if you have defects that large you should look at the inflated.nofix surface to see what they are.

What is your voxel resolution?

cheers
Bruce

On Tue, 22 Mar 2016, Dr Sampada Sinha wrote:

Thanks Bruce for your reply. I did run it thru' recon-all. It went for more than 2
days and then exited with XL defect error (convex hull was more than 14000 and vertex
size about 54000). So today I started by running the recon-all in parts. I did not
find anything wrong with brainmask files after running autorecon1. I am presently
running the autorecon-2 process. Will get back with the surf files when this process
is over.
Thank you again for your reply and support.

Kind regards,

Sampada

On Tuesday, March 22, 2016, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
sure. Have you tried running it through recon-all? It may work fine....
On
Tue, 22 Mar 2016, Dr Sampada Sinha wrote:

> Thanks Bruce for your reply. The acquisition was oblique and the voxel
size doesn't
> conform to the 1mm cube isotropic. I am trying to work on it and figure
out a
> solution. However, if I am not, hope its okay to send you the nifti
image.
> Thanks and regards,
>
> Sampada
>
>
>
> Rnday, March 20, 2016, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
> what do you mean by "adding" an oblique angle? If you mean
acquiring the
> data obliquely you should be fine as long as the voxels are close
to 1mm
> isotropic.
>
> cheers
> Bruce
> On Sun, 20 Mar 2016, Dr Sampada Sinha wrote:
>
> > Dear freesurfer experts,
> > Does adding an oblique angle during coronal or axial
acquisitions of
> T1w
> > images lead to topographical errors during mri_fix_topology
process?
> >
> > Thanks and regards,
> >
> > Sampada
> >
> >
> >
> > --
> > Sampada Sinha
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to
whom it
> is
> addressed. If you believe this e-mail was sent to you in error
and the
> e-mail
> contains patient information, please contact the Partners
Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent
to you in
> error
> but does not contain patient information, please contact the
sender and
> properly
> dispose of the e-mail.
>
>
>
> --
> Sampada Sinha
>
>
>
>
>
>
>
>
>
>
>
>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
Sampada Sinha