Hi Joana,
I agree with Eugenio that if this is failing from within python, then python is
probably messing with your environment. Based on that error log, it’s tough to
say whether this is a freesurfer problem or matlab. The fact that it runs fine
on linux seems to suggest it’s a macOS-specific issue with calling the matlab
runtime library from python. If you’re using anaconda or something, it might be
overwriting matlab-runtime linked libraries. I’m not sure how much we can help
out here, unfortunately.
Best,
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Joana Collet i Fàbregas
<joana.col...@gmail.com>
Date: Saturday, May 15, 2021 at 11:18 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] FreeSurfer error when running Hippocampal Subfields
External Email - Use Caution
Ok, thanks!
I forgot to mention ut before, but this error only occurs when running it in
IOS, in Linux it works fine...
El dv., 14 de maig 2021, 22:52, Iglesias Gonzalez, Juan E.
<jiglesiasgonza...@mgh.harvard.edu<mailto:jiglesiasgonza...@mgh.harvard.edu>>
va escriure:
Yes, but that doesn’t guarantee that the (library) environment is the same as
when you run something from the terminal.
I’m CCing Andrew Hoppes to see if he can assist.
Cheers,
/E
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
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On May 14, 2021, at 15:22, Joana Collet i Fàbregas
<joana.col...@gmail.com<mailto:joana.col...@gmail.com>> wrote:
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Dear Juan Eugenio,
I'm not sure what you mean. In Python I use os.system() to run the recon-all
command from the command line.
Thanks!
Joana
El dv., 14 de maig 2021, 21:04, Iglesias Gonzalez, Juan E.
<jiglesiasgonza...@mgh.harvard.edu<mailto:jiglesiasgonza...@mgh.harvard.edu>>
va escriure:
Dear Joana,
Is it possibly that Python changes somehow that libraries that are loaded,
compared with the command line?
Cheers,
/E
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
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On May 14, 2021, at 06:06, Joana Collet i Fàbregas
<joana.col...@gmail.com<mailto:joana.col...@gmail.com>> wrote:
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Good morning,
I am a Biomedical Engineering Student at Universitat de Barcelona and I am
creating a python script that has a Watchdog which detects new patients in a
specific folder, and we want it to run FS and Hippocampal Subfields. The FS
runs properly, but when the script arrives to the Hippocampal Subfields
command, it breaks.
When using the FreeSurfer's Hippocampal Subfields from a python script after
running FS recon-all right before, the processing is not performed due to the
error shown in the attatched file. However, when running the Hippocampal
Subfields from the terminal it does work.
We have even tried to create a watchdog only for the Hippocampal Subfields, and
when we move a folder obtained after running FS to a specific folder, it also
runs properly. It is only when it is concatenated with FS that it does not work.
We have contacted MathWorks Support, but they told us to reach you. The Matlab
versions we have are Matlab_R2020a and Matlab_R2014b.
Thanks a lot,
Joana Collet
<hippocampal-subfields-T1 (1).log><matlab_crash_dump.26817-2 - Jupyter Text
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