Sorry, just seeing that you also want cortical summaries. Those might be easier. You should run recon-all on the T1 template for the hammersmith. You can then create your own hammersmith annotation by mapping the atlas labels onto the surface (mri_vol2surf) and then mris_seg2annot. You can then use mris_apply_reg to map the annotation to the surface of an individual (or fsaverage).

Hi Freesurfer Developers,

 

Our group is hoping to obtain the cortical thickness, surface area, and volume for various cortical regions (as well as some subcortical volumes); however, we would like these values to be outputted with respect to the regions delineated in the Hammersmith atlas. This atlas is available for free online (http://brain-development.org/brain-atlases/adult-brain-maximum-probability-map-hammers-mith-atlas-n30r83-in-mni-space/) and I’ve included a screenshot to show you what files are included in the download. Based on this information, what is the best and/or most straight forward to move forward?

 

Thank you for your time. I look forward to hearing from you.

 

1. FreeSurfer version: freesurfer-i386-apple-darwin11.4.2-stable6-20170119
2. Platform: macOS High Sierra (Version 10.13.1)

 

Best,

 

Ryan

--

Ryan Flores

Clinical Research Coordinator

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