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-boun...@nmr.mgh.harvard.edu> on behalf of "Wakim,
Kathryn-Mary" <kathrynmary_wa...@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
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