Hi Glen, I think there is some confusion here about what this conversion is doing and what you want it to do. This conversion simply changes the way the information is stored, but it is still surface data. SPM/MRIcron cannot display surface data even if it is in nifti format. It sounds like what you want to to transform the surface data into volume data. For that you should use mri_surf2vol. doug

On 02/21/2013 05:17 PM, Glen Lee wrote:

Hi Doug, Just to re-assure your message below as I'm having the same issue,

I've converted an mgh file with a total of 163,842 vertices into a nifti file using . And it reshapes the structure to 3D as shown below.

fname: 'test_via_mr_conv.nii' dim: [27307 1 6] mat: [4x4 double] pinfo: [3x1 double] dt: [16 0] n: [1 1] descrip: 'FreeSurfer May 25 2011' private: [1x1 nifti]

The fact that I'm not able to display the nifti file in SPM or MRIcron means that the conversion to Nifti doesn't work correct?

• Glen

On Mon, Jan 28, 2013 at 2:09 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

How many vertices are on the surface? For nifti you have to
reshape the
size of the image so that it fits in the nifti format (requires
each dim
be less than 32k). If the number of vertices has a prime factor
that is
more than 32k, then you cannot convert it to nifti and use it in
another
software package (it still works in FreeSurfer, but then you could
just
use an mgh file then).
doug



On 01/28/2013 01:58 PM, Courtney Haswell wrote:
> Hi,
>
> Was there a resolution to this thread on the FreeSurfer mail
archive?
>
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg17886.html
>
> I am having the same issue trying to convert a cortical
thickness sig.mgh to
> a NIfTI file. I want to use the statistically significant area
as an ROI in
> another analysis.
>
> Thanks,
> Courtney Haswell
>
>

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
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