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November 01, 2021 09:28AM
Hello AFNI team,
I am having a few problems aligning macaques anatomical T1 to the template (3 out of 90 success, not bad!)
to resume:

- something not normal with aff_move_opt. It seems that you can only use one option and not combine multiple ones.

- _shft.nii.gz (not sure actually what is the command is producing this image) = far from the BASE. The orientation of the brain in T1 is not correct (mostly in SI axis in my case).
The mistake seems to happen when to orientation in the SI axis is far from the base despite that the two T1 images are centered.

- _shft_aff.nii.gz is almost well aligned to BASE but the little mistake generates big misalignments in the end.
- in my case, the misalignment is in the occipital areas

I can provide images if needed

Subject Author Posted

@animal_warper alignment issues

Doughboys November 01, 2021 09:28AM

Re: @animal_warper alignment issues

Doughboys November 01, 2021 01:58PM

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