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