Hi Chungmin

do you have a whole-brain T1 that you can use for generating anatomical models? If so, many more things are possible

cheers Bruce

On Thu, 8 Mar 2018, Chungmin Han wrote:

Dear whomever it may concern,

I'm Chungmin, a graduate research assistant in University of Texas at Austin, I'm fairly new to using freesurfer, I'd appreciate to get some advice on what I'm facing,

I have fMRI limited FOV collected on brainstem + little cerebellum/visual area, I've tried SPM manual registration to MNI space, falls in 1-2mm (1-2 voxels) away from accurate registering brainstem correctly,

is there a way to create transformation matrix optimized to fit brainstem in MNI space? Registering cortical region slightly bit wrong is okay to me at this moment,

https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures

I've noticed this has been posted pretty recently, but would like to figure out how to align in standard space for comparison.

I've also thought of inverse registering from MNI to each native space, however, if the transformation focuses on maximizing registration on the cortical level (T1) I don't think inverse registration solves the issue,

Thank you in advance :) Best

Chungmin

Chungmin Han

Graduate Research Assistant

The University of Texas at Austin 204 E. Dean Keeton St Austin TX 78712 Mobile: 512-717-1671