[Freesurfer] Extraction of cortical thickness in native space

Hello,

We are attempting to extract cortical thickness values from a pre-defined ROI in MNI space.

Originally, we had followed the instructions detailed here:

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

for extraction in MNI space, but now wanted to extract thickness from individual subject T1 images in native space.

We attempted to use the same pipeline (e.g. register native space T1 to fsaverage) but were unable to get a good registration with several different tools.

Is there a better way to do this, either by improving the registration to fsaverage, or by transforming the ROI to native space (which we have done) and projecting that to a surface/label?

Any suggestions are welcome, and we appreciate the help!

Cheers,

Dan

VolumeRoiCorticalThickness - Free Surfer Wikihttps://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness surfer.nmr.mgh.harvard.edu Cortical Thickness of a Volume-defined ROI. This page describes the workflow to extract freesurfer cortical thickness values for a region-of-interest (ROI) defined in ...