You have effectively applied the registration twice, once when you ran bbregister to get the output and once when you ran tkregister2 with --reg. Try that tkrister2 command with func.nii.gz as the --mov

On 1/21/19 6:35 PM, Sam W. wrote:

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Hello,

I have registered example_func.nii.gz to the anatomical image using bbregister and then I looked at the registered file with tkregister2.

$ bbregister --bold --lta reg.lta --mov example_func.nii.gz --s sub001 --o f-in-anat.nii.gz $ tkregister2 --s sub001 --mov f-in-anat.nii.gz --reg reg.lta --surf

However if I click "coronal" tkregister2 shows the coronal surface as expected, whereas it shows the horizontal volume. If I click "horizontal" it shows the horizontal surface, whereas it shows the coronal volume. When I click "sagittal" the sagittal surface and volume are loaded, but the orientations are different. When I use the example_func as the mov image in tkregister2 I don't get this issue. I don't understand why the registered image "f-in-anat.nii.gz" is not aligned with the anatomical image with the tkregister2 command, because "f-in-anat.nii.gz" is exactly the output image of the bbregister transformation from functional to anatomical space, isn't it? Could someone please help me understand this?

Thanks Sam

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