Hi Kamy,

The QA tools are actually developed outside of our lab. It might be helpful to contact the Reuter lab directly - https://github.com/Deep-MI/qatools-python

best

Andrew

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Wakim, Kathryn-Mary" <KathrynMary_Wakim@urmc.rochester.edu>
Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, July 9, 2020 at 7:51 PM
To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] QAtools with Freesurfer version 6.0

        External Email - Use Caution        

Hi all,

I’m relatively new to Freesurfer, and I am just beginning to check the output of my recon-alls using QAtools. However, I’m running into a number of difficulties and errors with QAtools, and I’m wondering if this tool is not yet optimized for the current version of Freesurfer.

I have attached the recon_checker.All.summary.log output from QA tools. Below, I’ve also highlighted some of the errors and issues I see in the recon_chcker log file. Please note thatt, per the subject’s recon-all log file, recon-all ran to completion with no errors.

Overview of recon_checker errors:

1) ERROR: Subject 10201003 missing output file ../mri/nu_noneck.mgz

• Note: this is repeated for a number of different output files

2) ERROR: Recon-all steps missing in subject 10201003 status file

3) View your snapshots by opening this file in an internet browser:

• Note: I have attached a screenshot of the output .html file in-browser. Note that I have installed and verified installation of ImageMagick.

Thank you very much for your help,

Kamy Wakim