Hi Navid, it is still not clear what you want. Each surface coordinate has an xyz. This space that this xyz is in is a peculiar space defined by FS. You want to use a different xyz space. It could be scanner space. It could be col-row-slice of your axial data. Or is it that you just want to visualize the surfaces on the axial. In that case, you'll have to indicate what tool you are going to use (you cannot use tkmedit for this -- it will just conform it to 256^3).

doug

Navid Shiee wrote:

Hi, Thanks for your reply. I make an examaple to clarify myself. I have a 256x256x128 axial image which has 0.83^3 resolution. I am intrested in generating the cortical surfaces and overlay it on this image. Freesurfer first converts this image to 256^3 voxels and 1^3 resolution and then generates the surfaces. Thus if I want to intersect freesurfer surfaces with my axial data, I can not because surface is in a different space. Is there a way to transform the freesurfer surfaces to 256x256x256 axial space? Thanks a lot for your help.

Navid

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-----Original message-----

*From: *Douglas N Greve <greve@nmr.mgh.harvard.edu>*
To: *Navid Shiee <navid@jhu.edu>*
Cc: *freesurfer@nmr.mgh.harvard.edu*
Sent: *Tue, Aug 30, 2011 20:13:09 GMT+00:00*
Subject: *Re: [Freesurfer] Freesurfer surfaces in the original space


Hi Navid, what do you mean by "the original image space"? Ie, what
coordinates do you specifically want? Voxel? Scanner?
doug

Navid Shiee wrote:
> Dear Freesurfer team,
>
> I have a question regarding Freesurfer surfaces. I submitted this
> questions to the wiki but did not get any response and I was
wondering
> if you can help me on this issue.
> I am doing some experiments with Freesurfer and would like to have
> surfaces in the original image space. FS converts everything to
1mm^3
> 256x256x256 grid in the coronal space. I have axial images which
does
> not have homogenous grid (although it has isotropic resolution). I
> know there is a command to convert the volumetric structural
> segmentation into the original space but could not find the command
> for surfaces. I would be very grateful if you can provide me
with some
> information for doing this.
>
> I appreciate your kind help in advance.
>
> Regards,
>
> --
> Navid Shiee
> Ph.D. Candidate
> Laboratory of MEDical Image Computing (MEDIC)
> Image Analysis and Communication Laboratory (IACL)
> Johns Hopkins University
>
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>
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> Freesurfer@nmr.mgh.harvard.edu
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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