nope, the brainmask hasn't been transformed, but the transform has been computed (and stored in the talairach.xfm file), so brainmask itself is not in talairach coordinates. You can transform it by specifying -at transforms/talairach.xfm to mri_convert (-at == apply_transform).

cheers, Bruce On Mon, 4 Sep 2006, Lee HL wrote:

Hi Bruce, If I understand correctly, since the brainmask.mgz image has been normalized to the MNI-talairach template, the coordinate (0, 0, 0) should correspond to the anterior commissure point, right? Sorry for the trouble. Cheers, HweeLing

On 9/4/06 8:54 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:

...

He HweeLing,

what kind of coordinate do you mean? If it's just the voxel coord, then I don't think it matters.

cheers, Bruce

On Mon, 4 Sep 2006, Lee HL wrote:

...

Hi Bruce and all,

I wish to convert the MGZ format image into ANALYZE format image.

I used the command line to convert the MGZ format image: "mri_convert -i brainmask.mgz -o brainmask.img --out_type spm".

When I display the image using SPM, the coordinate (0, 0, 0) appears at the posterior commissure. However, when I display the mgz format image using tkmedit, the coordinate (0, 0, 0) appears at the anterior commissure.

Was I using the correct command line to convert the image?

Thanks!

Cheers, HweeLing

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