Hi Keith, what version of ubuntu are you using?

 

Best

Andrew

 

From: "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ@mgh.harvard.edu>
Date: Friday, December 4, 2020 at 4:42 PM
To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Cc: "Hoopes, Andrew" <AHOOPES@mgh.harvard.edu>
Subject: Re: [Freesurfer] segmentHA_T1.sh failing {Disarmed}

 

Dear Keith,

It is a license problem. The hippo/amygdala module relies on mri_robust_register for initialization, and this program is failing due to the aforementioned license problem. Once that has been fixed, the hippocampal module should be fine.

Regarding the license problem: I have no idea, but I am CCing Andrew Hoopes, who hopefully will be able to help.

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.edu> on behalf of Keith Harenski <kharenski@mrn.org>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Friday, December 4, 2020 at 16:24
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] segmentHA_T1.sh failing {Disarmed}

 

        External Email - Use Caution        

Hello,

 

I am getting a strange message when trying to run the amygdala and hippocampal sementations, even when attempting to run the script on someone who the script previously completed.

 

When it starts, the script immediately displays the following message:

error parsing license file, expected 4 values

 

The license error message further instructs libc requires a newly formatted license so I got a new one. The new one is identical to the original however and it has four entries - my email address, a five digit number, followed by two alphanumeric strings.. 

 

The script then seems to start, will run for about 30 seconds or so then stop again with the following message:

Error using segmentSubjectT1_autoEstimateAlveusML (line 533)
Fitting mesh to synthetic image resulted in no deformation

...

T1 hippocampal subfields exited with ERRORS at Thu Dec  3 15:56:32 MST 2020

 

I get slightly different errors when running on another subject, who like the one above, previously completed. For this subject the license error is more persistent:

error parsing license file, expected 4 values

 

I've attached the hippocampal-subfields-T1.log for the first subject as it contains the full output.

Thank you,
Keith

--

Keith Harenski
Mobile MRI Manager
Mobile MRI Core and Clinical Cognitive Neuroscience Laboratory