mris_sphere: segmentation fault (core dumped)

[Miguel Ángel Rivas Fernández]

Dear experts,

I ran the recon-all command in one subject and I get one error in mris_sphere (please, see the attached file). Sorry, I tried to find the solution in previous posts to avoid repeat the same questions but I did not find a solution. The only suggestion that I found https://groups.google.com/a/humanconnectome.org/g/hcp-users/c/Y1ciC0Pztq8/m/9oOsPsAfAAAJ is cleaning out the FreeSurfer files and rerunning thre recon-all but unfortunately this did not work. I have repeated it several times and it always stops at the same point in the recon-all.

Below you can find some characteristics of the computer I am using.

Number of cores: 20

Threads per core: 2

Thank you very much in advance.

Best regards,

[Tim Coalson]

The log file mentions freesurfer 6.0.0.  Have you tried freesurfer 6.0.1?

Tim

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[Miguel Ángel Rivas Fernández]

Hi Tim,

No, I did not try that FreeSurfer version. I will try this version and I will send you a message if it happens the same error.

Thanks for your help.

Best regards

Miguel

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[Miguel Ángel Rivas Fernández]

Dear Tim,

I tried with the FreeSurfer 6.0.1 version and it worked sometimes only with few subjects. The error occurs again in the mris_sphere (please, see the attached file). I am not an expert in this matter but could this error be related to the number of cores being used in the recon-all or to a memory problem (e.g. swap)? It seems strange that it works in some cases and not in others .... Also, I think that this computer has enough features to be able to run recon-all without problems (even if I ran the recon-all on several terminals at the same time).

Any help would be very appreciated.

Thank you very much.

Best regards,

[Glasser, Matt]

Is it reproducible which subjects have the error, if not perhaps you should test the RAM on the computer.

Matt.

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