Re: [Freesurfer] Regarding: oblique view

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

javascript:;> 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
  >
  >
  >
  >
  >
  >
  >
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  >
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