Hi Doug,

Thank you for your response. I attempted to run recon-all on the Hammersmith nifti file as suggested, but unfortunately it appears to have run into some issues. I’ve attached the recon-all.log for reference.

Best,

Ryan

Ryan Flores

Clinical Research Coordinator

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas Greve <dgreve@mgh.harvard.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, April 17, 2018 at 9:33 AM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Recon-all w/ Hammersmith atlas

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).

On 4/16/18 3:14 PM, Ryan Flores wrote:

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.

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

Best,

Ryan

--

Ryan Flores

Clinical Research Coordinator
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