It is happening on every subject; the disk isn't full. I checked the MRI folder, and some of the files (nu.mgz, brainmask.mgz) weren't outputted. For one participant who had also been processed on another computer I copied these files onto the cluster and it seems to run ok once these files are in the folder. I found a similar problem (https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-January/027257.ht...) and have asked the team who maintain the cluster to try this solution as I don't have the right permissions. Hopefully this will solve the issue.

Thanks for your help, Eileanoir

-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Rudolph Pienaar Sent: 28 November 2013 00:47 To: Douglas N Greve; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_calc recon-all problem

Not sure if it's relevant, but the syntax for mris_calc in this case is:

mris_calc -o <outputFile> <file1> mul <file2>

Your log is missing <file2> so the syntax doesn't make sense and mris_calc will fail...

On 11/27/13, 18:10 , Douglas N Greve wrote:

Does it happen on every subject? Any chance that the disk is full?

On 11/27/2013 07:43 AM, Johnson, Eileanoir wrote:

...

Hi there,

I am currently trying to run freesurfer version 5.3.0 on a cluster and am encountering an error when running recon-all.

The error is:

Writing to ./tmp.mri_nu_correct.mni.2867/output.mean.dat

mri_segstats done

mris_calc -o ./tmp.mri_nu_correct.mni.2867/nu2.mnc ./tmp.mri_nu_correct.mni.2867/nu2.mnc mul

Linux blue34 2.6.18-164.6.1.el5 #1 SMP Tue Oct 27 11:28:30 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s 22057 exited with ERRORS at Wed Nov 27 12:31:54 GMT 2013

Does anyone know what might be causing recon-all to exit at this point? I have attached the full log file.

Thanks,

Eli

Eli Johnson Research Assistant, Track-On UCL Institute of Neurology, Box 104 Queen Square, London, WC1N 3BG Tel:+44(0)207 242 0038

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- Rudolph Pienaar, M.Eng, D.Eng / email: rudolph@nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.