Hi Meng,

On 04/30/2013 09:53 PM, limengsecret wrote:

> Hi Doug,

> Thanks for your reply.

> I have downloaded some freesurfer files (.annot, .label, .curv, .w)

> about the specific regions.

what do you mean you downloaded them? where did they come from exactly?

Are they your own data?

> And I want to convert this files to volumetric masks, then the masks

> are used to overlay the normalized functional data, and according to

> the mask to define the specific region as roi.

How was your functional data normalized? Specifically what atlas was used?

> Thus, the problem is that, how I can achieve this goal, and which

> commands should I use.

> Thanks a lot.

> Best wishes,

> Meng

> Date: Mon, 29 Apr 2013 17:30:14 -0400

> From: Douglas N Greve <greve@nmr.mgh.harvard.edu>

> Subject: Re: [Freesurfer] convert labels to volumetric masks

> To: freesurfer@nmr.mgh.harvard.edu

> Message-ID: <517EE666.8050301@nmr.mgh.harvard.edu>

> Content-Type: text/plain; charset=UTF-8; format=flowed

> Hi Meng,

> I don't understand what you are trying to do. Can you

> elaborate? That command will simply check a registration that already

> exists.

> doug

> On 04/29/2013 10:36 AM, limengsecret wrote:

> Dear FreeSurfers,

> I want to convert cortical labels to volumetric masks, the mask

> created are used to register with the normalized functional data and

> to define the roi, so could I run the following command?

> tkregister2 -mov sub/func.nii -noedit -s fsaverage -regheader -reg

> ./register.dat/

> and the func.nii has been normalized (sub.nii) to the MNI space. And

> if the command is wrong, which command should I use?

> Best wishes,

> Meng

Douglas N. Greve, Ph.D.

MGH-NMR Center

greve@nmr.mgh.harvard.edu

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Hi Doug,

The relative freesurfer files were downloaded from http://ltl.tkk.fi/wiki/Atlas about the retinotopic visual areas. And I want to convert the files to volumetric masks to use for my own data.

The functional data have been preprocessed with slice-timing, realignment, and normalization. And the masks overlay the functional data created above to define the retinotopic visual areas.

Thank you!