You can manually change the registration in tkregisterfv. But we rarely see this happen and I'm wondering if it might be some other problem. Are you totally sure that the anatomical and PET come from the same subject?

On 10/3/2019 12:59 PM, Vicky Yang wrote:

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Hi Doug,

Thanks for your respond! I ran the the command with debug flag and figured out the problem. It is because I use a space in the name of the PET data directory. After removing the space character, tkregisterfv works great!

But one PET image didn't register well with T1. Is there any way to improve the registration?

Thanks again for your time!

Regards,

Vicky
On Wed, Oct 2, 2019 at 5:36 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu> wrote:
Can you run
tkregisterfv --debug --mov pet.nii.gz --targ T1.nii --reg pet_T1.reg.lta
and send the terminal output?

On 10/2/2019 3:58 PM, Vicky Yang wrote:
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Dear Freesurfer experts,

I used mri_coreg to register my pet data to T1 like below:

mri_coreg --mov pet.nii.gz --ref T1.nii --reg pet_T1.reg.lta

After coregistering, I checked the registration using tkregisterfv like below:

tkregisterfv --mov pet.nii.gz --targ T1.nii --reg pet_T1.reg.lta

However, the command didn't work with an error:

if: Expression Syntax.

Any suggestions would be appreciated. Thank you in advance for your help.

Sincerely,

Vicky
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