Hi Sofia

Unfortunately that doesn’t really work as the most time-intensive steps are required. We are working on replacing some of these with deep-learning equivalents, but it will be some months before that is available.

Sorry

Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Nikolaidou, Sofia
Sent: Friday, May 12, 2023 3:34 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all for GM quantification

External Email - Use Caution

Good afternoon,

My name is Sofia and I work with Drs. Eva Ratai and Lilly Mujica-Parodi on the DCC project. I am reaching out to ask for your advice on a FreeSurfer question.

I am using recon-all to try to quantify and compare GM volume and mean thickness among our subjects. In essence, I think I have all the necessary measurements in the outcome files titled aseg.stats and ?h.aparc.stats. Would you happen to know how I can customize the stream and reduce the processing time by taking out steps from the -all process? In other words, what would be the minimal set of steps that I have to run in order to acquire the above output files?

Thank you in advance!

Kindly,

Sofia

Sofia Nikolaidou | Clinical Research Coordinator

MGH/HST Martinos Center for Biomedical Imaging

149 13^th St, Charlestown, MA 02129
Phone: 617-417-4463
snikolaidou@mgh.harvard.edu