[Freesurfer] Freeview mghRead error

[Duvnjak, Aleksandar]

External Email - Use Caution

Dear Freesurfer Developers,

I have recently switched to a Mac for ease of use and have encountered an error 
upon trying to view output files from a previous data cohort which were 
processed on a remote computing server and copied to this Mac's local drive. I 
am able to view all surfaces and volumes of the native bert tutorial set, 
however am unable to view my own outputs.

In the terminal I receive the following error:


Katarinas-MacBook-Pro:mdc026 kduvnjak$ freeview -v 
/Applications/freesurfer/subjects/mdc026/mri/wm.mgz

mghRead(/Applications/freesurfer/subjects/mdc026/mri/wm.mgz, -1): could not 
open file

MRIread failed: Unable to read from 
/Applications/freesurfer/subjects/mdc026/mri/wm.mgz

mghRead(/Applications/freesurfer/subjects/mdc026/mri/wm.mgz, -1): could not 
open file

2021-06-02 11:07:49.903 Freeview[6760:441577] modalSession has been exited 
prematurely - check for a reentrant call to endModalSession:

Please find below any additional relevant information:

Freesurfer version: freesurfer-i386-apple-darwin11.4.2-stable6-20170119 
(freesurfer-Darwin-OSX-stable-pub-v6.0.0.dmg)
Platform: macOS Sierra Version 10.12.6
uname -a:

Darwin Katarinas-MacBook-Pro.local 16.7.0 Darwin Kernel Version 16.7.0: Thu Dec 
20 21:53:35 PST 2018; root:xnu-3789.73.31~1/RELEASE_X86_64 x86_64

I am also strangely unable to attach the recon-all file to this email. Perhaps 
this is some sort of permissions issue, although I have sudo chown for this 
user on the dir and that didn't seem to help.

Kind regards,
Aleksandar
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Re: [Freesurfer] hippocampal-subfields-T1 error

[Duvnjak, Aleksandar]

External Email - Use Caution

To clarify, upon copying the entire FreeSurfer 6.0 package to our personal 
directory, we have then downloaded the matlab runtime MCRv80 folder to that 
directory and the issue does not appear to be the hippocampal-subfields-T1 
pipeline accessing that.

Regards,
Aleks Duvnjak

From: Duvnjak, Aleksandar
Sent: 27 March 2020 18:38
To: freesurfer@nmr.mgh.harvard.edu 
Subject: hippocampal-subfields-T1 error

Dear FreeSurfer Experts,

FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0
Platform: Secure Shell port of a high performance computer (HPC) accessed via 
Ubuntu 18.04 WSL

Having processed a cohort of 1mm^3 MRI images via the recon-all command, we 
have had issues processing the hippocampal subfield command as described: 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields

Although we eventually want to run the command in array, we are currently 
attempting it on individual subjects to ensure a good output. Upon running the 
command we receive a "permission denied" error. The HPC is a shared cluster, 
and the FreeSurfer 6.0.0 app is downloaded in a shared dir which we cannot 
edit, and thus couldn't download the Matlab runtime to.

We initially thought this may be the issue, and so tried multiple workarounds, 
including copying the entirety of the FreeSurfer installation package from the 
shared directory to our own directory, within which we have editing 
permissions. This didn't help, even when setting our personal directory as the 
FREESURFER_HOME. As you can see from the end of the recon-all.log file, we 
tried numerous attempts with various workarounds and all have the same outcome.

I appreciate this may still be more of an issue with running FreeSurfer via a 
secure shell port to a HPC cluster rather than an issue with FreeSurfer itself, 
but I'm sure you have many research labs asking questions regarding using HPC 
systems to run FreeSurfer, so any recommendations or thoughts would be welcome.

Kind Regards,
Aleks Duvnjak
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Re: [Freesurfer] hippocampal-subfields-T1 error

[Duvnjak, Aleksandar]

External Email - Use Caution

Dear Juan,

Thank you so much. This has sorted our issue. You're a lifesaver.

Kind regards,
Aleks Duvnjak

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Iglesias Gonzalez, Juan 
E. 
Sent: 27 March 2020 19:07
To: Freesurfer support list 
Subject: Re: [Freesurfer] hippocampal-subfields-T1 error


This email from jiglesiasgonza...@mgh.harvard.edu originates from outside 
Imperial. Do not click on links and attachments unless you recognise the 
sender. If you trust the sender, add them to your safe senders 
list<https://spam.ic.ac.uk/SpamConsole/Senders.aspx> to disable email stamping 
for this address.



Dear Aleks,

Please try:  chmod u+x /rds/general/project/amyloidpet/live/freesurfer/bin/*

Cheers,

/Eugenio





Juan Eugenio Iglesias

Senior research fellow

CMIC (UCL), MGH (HMS) and CSAIL (MIT)

http://www.jeiglesias.com







From:  on behalf of "Duvnjak, 
Aleksandar" 
Reply-To: Freesurfer support list 
Date: Friday, March 27, 2020 at 14:39
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] hippocampal-subfields-T1 error



External Email - Use Caution

Dear FreeSurfer Experts,



FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0

Platform: Secure Shell port of a high performance computer (HPC) accessed via 
Ubuntu 18.04 WSL



Having processed a cohort of 1mm^3 MRI images via the recon-all command, we 
have had issues processing the hippocampal subfield command as described: 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields



Although we eventually want to run the command in array, we are currently 
attempting it on individual subjects to ensure a good output. Upon running the 
command we receive a "permission denied" error. The HPC is a shared cluster, 
and the FreeSurfer 6.0.0 app is downloaded in a shared dir which we cannot 
edit, and thus couldn't download the Matlab runtime to.



We initially thought this may be the issue, and so tried multiple workarounds, 
including copying the entirety of the FreeSurfer installation package from the 
shared directory to our own directory, within which we have editing 
permissions. This didn't help, even when setting our personal directory as the 
FREESURFER_HOME. As you can see from the end of the recon-all.log file, we 
tried numerous attempts with various workarounds and all have the same outcome.



I appreciate this may still be more of an issue with running FreeSurfer via a 
secure shell port to a HPC cluster rather than an issue with FreeSurfer itself, 
but I'm sure you have many research labs asking questions regarding using HPC 
systems to run FreeSurfer, so any recommendations or thoughts would be welcome.



Kind Regards,
Aleks Duvnjak
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