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.edumailto: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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When you say that you changed the scale, what do you mean? Are you sure that the PET voxel size is accurate? Something else you can try is to specify --dof 9 when you run mri_coreg -- this will fit the scale as well as the translation and rotation.

On 10/7/2019 1:51 PM, Vicky Yang wrote:

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Hi Doug,

I am sure that the anatomical and PET come from the same subject. And I am using the same processing procedures as worked well on other 7 subjects. So I don't think it is because of processing or mixing data.

According to the co-registered result, The skull in PET image is wider than the anatomical image but the ventricle part seemed OK. I have to manually change the x scale in PET image from 1 to 0.925 to match the anatomical image.

I can certainly manually change the registration in tkregisterfv but it would be more satisfying to understand why it is going awry. And suggestions?

Thanks, Vicky

On Mon, Oct 7, 2019 at 11:21 AM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> wrote: 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:

External Email - Use Caution

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.edumailto: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:

External Email - Use Caution

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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