[Freesurfer] tkregister2 - horizontal and coronal inverted in the functional only

[Ilaria Sani]

Dear All,

I have a functional and a T1 registered, but they are not in anatomical 
coordinates.
I put the anatomical in the desired position by using tkregister2.
I was hoping to use the output reg file to re-position the functional as well.

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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Re: [Freesurfer] tkregister2 - horizontal and coronal inverted in the functional only

[Douglas Greve]

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?

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 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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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] tkregister2 - horizontal and coronal inverted in the functional only

[Ilaria Sani]

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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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.