Hi Eugenio,
Thank you so much for your response! I did use the development version to run the command. Would you have any other ideas what the possible cause might be?
Best, Wisteria
Date: Tue, 7 Jan 2020 09:05:32 +0000 From: "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ@mgh.harvard.edumailto:JIGLESIASGONZALEZ@mgh.harvard.edu> Subject: Re: [Freesurfer] Amygdala Segmentation T1.v20 Command To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <8970525B-ED9A-4F56-901A-50F5787C925D@mgh.harvard.edumailto:8970525B-ED9A-4F56-901A-50F5787C925D@mgh.harvard.edu> Content-Type: text/plain; charset="utf-8"
Dear Wisteria, Did you run the command segmentHA_T1.sh on those subjects using the development version? Cheers, /Eugenio
Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Deng, Yushan Wisteria" <YWDENG@mgh.harvard.edumailto:YWDENG@mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Friday, 3 January 2020 at 20:31 To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Amygdala Segmentation T1.v20 Command
Dear Freesurfer experts,
Happy new year!
I encountered an issue with the quantifyHAsubregions.sh command as I tried to extract amygdala subnuclei values from a previously segmented dataset. I tried both commands below, specifying the version (v20) and not: quantifyHAsubregions.sh amygNuc T1 All_Amyg [subjects_dir] quantifyHAsubregions.sh amygNuc T1.v20 All_Amyg [subjects_dir]
The command did not run. No error message was given. It just skipped to a new command line. Please see attached for a screenshot.
The recon was done in Freesurfer 5.3 and the sample size is very big (~1400). I wonder if that or anything else could be causing the problem. Any guidance is immensely appreciated!
Thank you! Wisteria
Wisteria Deng Clinical Research Coordinator Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, Rm 2611 Charlestown, MA 02129 Phone: 617-643-4441