Hi,
The coordinates here are in our internal coordinate convention, which is the same as scaled voxel coordinates when the image has a "radiological-orientation" (negative determinant of the qform or sform matrix). Otherwise there is also a swap in the x voxel coordinate (x_new = N_x - 1 - x_old).
I hope this helps.
All the best,
Mark
> On 15 Jun 2018, at 20:14, Gabriel Benigno <[log in to unmask]> wrote:
>
> Hello,
>
> I am in the process of adapting the PreFreeSurfer pipeline for marmoset primates. Currently, I am on the ACPC alignment step, and it seems that the AC and PC coordinates in the aff2rigid function require custom values for the marmoset brain.
>
> I would like to ask about the nature of the coordinates of the three vectors of the AC ([91, 129, 67, 1]), the PC ([91,100,70,1]), and the point above the AC in the mid-sagittal plane ([91,129,117,1]). Are these scaled mm coordinates of the MNI152 0.7mm template? A brief explanation would be greatly appreciated.
>
> Sincerely,
> Gabriel
>
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