Dear Akila,
The error stems from trying to write the outpus of –qc and –vol to the same CSV file.
We’ll add a check to the code to make sure that an error is thrown if both files are the same.
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
http://www.jeiglesias.com
From:
freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Weerasekera, Akila,PHD <AWEERASEKERA@mgh.harvard.edu>
Date: Tuesday, October 3, 2023 at 6:21 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] SynthSeg volume labels
External Email - Use Caution
Thanks Eugenio! csv attached...
I source:
best,
Akila
Akila Weerasekera, PhD | Postdoctoral Research Fellow
Maria Mody lab for Developmental Language and Reading Research Laboratory |
Eva Ratai Lab for Clinical Spectroscopy |
Garry Nolan Lab (Stanford University) |
Harvard Medical School | A. A. Martinos Center for Biomedical Imaging | Massachusetts General Hospital | 149 Thirteenth Street, Room 1101 |Charlestown, MA 02129, USA
Mobile: (781) 820 4501
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edu>
Sent: Tuesday, October 3, 2023 8:52 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] SynthSeg volume labels
External Email - Use Caution
Thanks, this is super weird. When did you download this dev version? Also: would it be possible to share the CSV file, please?
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
http://www.jeiglesias.com
From:
freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Weerasekera, Akila,PHD <AWEERASEKERA@mgh.harvard.edu>
Date: Tuesday, October 3, 2023 at 7:01 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] SynthSeg volume labels
External Email - Use Caution
Hi,
Using SynthSeg (Freesurfer dev) with --vol, the .csv does not contain all volume labels, do I need to include anything
else in the command?
Thank you,
Akila
Akila Weerasekera, PhD | Postdoctoral Research Fellow
Maria Mody lab for Developmental Language and Reading Research Laboratory |
Eva Ratai Lab for Clinical Spectroscopy |
Garry Nolan Lab (Stanford University) |
Harvard Medical School | A. A. Martinos Center for Biomedical Imaging | Massachusetts General Hospital | 149 Thirteenth Street, Room 1101 |Charlestown, MA 02129, USA
Mobile: (781) 820 4501