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To follow up on this, it seems the issue is related to where the data are stored on the user’s server and perhaps the filesystem/mode of access being used. There does not seem to be any issue with Ubuntu generally, as processing works fine on the user’s OS drive…

Matt.

From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Jayasekera, Dinal" <dinal.jayasekera@wustl.edumailto:dinal.jayasekera@wustl.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, April 11, 2019 at 12:11 PM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] nu_correct crashing in FreeSurfer v6.0

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Douglas,

I've run the recon-all script with images from patients that were previously run using FreeSurfer 5.3.0 and I received the same error.

I haven't run it outside of the HCP pipeline. I can attempt that to see if it gives a different result. I'm not exactly sure how to go about doing this. Could you advise me on the best sequence of actions to take?

Kind regards, Dinal Jayasekerahttps://dinaljay.weebly.com/

PhD Candidate | InSITE Fellowhttps://www.insitefellows.org/ Ammar Hawasli Labhttps://hawaslilab.weebly.com/ Department of Biomedical Engineeringhttps://bme.wustl.edu/Pages/default.aspx | Washington University in St. Louishttps://wustl.edu/

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> Sent: Wednesday, April 10, 2019 5:27:15 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] nu_correct crashing in FreeSurfer v6.0

Have you looked at the images to verify that there are no major problems with it? Can you run it outside of the HCP pipeline to make sure it is not an interaction?

On 4/8/19 12:52 PM, Jayasekera, Dinal wrote:

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Dear all,

I have been running version 4 of the HCP Pipelines which now used FreeSurfer 6.0. I get the following error when running recon-all using their FreeSurferPipelineBatch script:

/nu_evaluate: crashed while running minc_modify_header (termination status=134)/ /nu_correct: crashed while running nu_evaluate (termination status=65280)/ /ERROR: nu_correct/

I didn't get this error previously when running FreeSurfer 5.3.0 on the same set of data. Are the MNI tools distributed through FreeSurfer 6.0 sensitive to the operating system and its version? Does anyone have a record of it working on an Ubuntu 14.04 OS?

1. FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0
2. Platform: Ubuntu 14.04
3. recon-all.log: see attached

Kind regards,

*Dinal Jayasekera https://dinaljay.weebly.com/*

PhD Candidate | InSITE Fellow https://www.insitefellows.org/ Ammar Hawasli Lab https://hawaslilab.weebly.com/ Department of Biomedical Engineering https://bme.wustl.edu/Pages/default.aspx | Washington University in St. Louis https://wustl.edu/

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