Hi,
> i have 2 questions:
>
> 1. what is the space for the vertices in the meshes produced by FIRST? is it voxel index or native mm?
Neither. It is a scaled (voxel) coordinate system - in mm - (i.e. the voxel coordinates just multiplied by the voxel sizes
in mm so that the voxel origin coincides with the scale coordinate origin). Also, the voxel coordinates are only the
same as the nifti voxel coordinates if the qform/sform has a negative determinant. Otherwise the x-voxel coordinate
is flipped.
> 2. somewhere during the processing, there's a .mat matrix produced which moves my subject data to MNI space. Given that the .nii files have already a matrix to move from voxel index to native mm, does this .mat matrix move the subject data from voxel space to MNI space, or from native mm into MNI space?
As above, the matrix maps scaled coordinates between images. These are FLIRT matrices and the convention for
these is described in previous posts, and is not the easiest thing to work with. I would advise using our tools (flirt,
img2imgcoord, std2imgcoord, etc) to deal with them rather than reinventing this wheel if possible.
All the best,
Mark
>
> thank you!
> roberto
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