Sent: Sunday, February 7, 2016 10:44 PM

On 2/5/16 12:49 PM, Ilaria Sani wrote:

Dear All,

I have a functional and a T1 registered, but they are not in anatomical coordinates.

Do you mean neither are in the "conformed" 256^3, 1mm^3 FreeSurfer coordinates?

Both the T1 and the functional are "conformed" 256^3, 1mm^3

I put the anatomical in the desired position by using tkregister2.

Was the T1 used to generate the FS results? If so, why do you need to get it into FS coordinates? If not, then use bbregister to create the registration file, then use mri_vol2vol to map it into FS space.

I'm working with multimodal data. I acquired DTI data and inherited the T1 and the functional.
The T1 was previously used for other purposes and it came in different coordinates.
I used tkregister2 and mri_vol2vol to put the T1 in Talairach coordinates and create the registration file.
Then, I used the reoriented T1 to get gray-white matter segmentation.
Now I would like to apply the same registration to the functional and place seeds in the DTI data.
When I do so, the output image has the coronal and horizontal view inverted.
How can I solve this problem?

Thanks,
Ilaria

I was hoping to use the output reg file to re-position the functional as well.

Use bbregister to register the functional to FS coordinates, then again use mri_vol2vol.

I got an unexpected output!
The functional looks reoriented BUT, coronal is horizontal, horizontal is coronal and sagittal is 90deg rotated.

How did it happen and how can I fix the problem?

Thanks,

Ilaria
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