Transform High-Resolition T2 to MNI space

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Hi all,

I’m wondering if there is a way to transform a high-resolution T2 image to MNI space? Python code is preferred but other software could also work.

Thanks,
Lily

2

Hi, Lily-

You can use AFNI’s 3dQwarp with the “lpc” cost function. This is a nonlinear alignment program, and this particular cost function is good for aligning datasets of differing contrasts (such as a T1w template and a T2w subject anatomical).

While not a Python approach, you can call command line tools from Python (e.g., with subprocess).

–pt

1 Like
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That makes sense. Thank you, pt!