Is your $FSLDIR environment variable set?

On 04/22/2016 02:09 PM, Mcnorgan, Christopher wrote:

That doesn't seem to be the problem. Attached are the file listings for the /usr/bin directory for fsl* for the working and not working computers. The symlinks for fsl binaries on both computers point to the same place, and I can run something like fslview on both computers. ________________________________________ From: Douglas N Greve greve@nmr.mgh.harvard.edu Sent: Friday, April 22, 2016 1:54 PM To: Mcnorgan, Christopher Subject: Re: [Freesurfer] preproc-sess error opening tmp brain_mask

Do you have FSL installed on the machines that work and not on the machine that does not work?

On 04/22/2016 01:49 PM, Mcnorgan, Christopher wrote:

...

Hi Doug,

Thanks for your generous time donation resolving this problem. There was a delay in getting this diagnostic information to you (which is itself diagnostic) because prior to your response, I retraced my steps preparing the data for running FS-FAST using my wiki checklist, but on a different computer. After rerunning mkanalysis-sess, mkcontrast-sess, double-checking my par-files and any other related files that needed to exist, I reran preproc-sess on FS_T1_501 without incident ... on a different machine.

This suggested that either I made a mistake that I fixed on my do-over, or else that the error is machine-specific. I'm repeating the procedure on data for the same participant doing the same task collected on the same scanner at time point 2, so the subject in question is FS_T2_501. Again I come to the same failure on the machine that seems to be giving me problems.

I've attached the dng.log file you requested. I hope it has some useful clues. If you need to know anything about the particular computer configuration, let me know, though two other machines that work are similarly configured (one has identical hardware and all are accessing the fMRI data stored on a remote server on a cifs share mounted at ~/ubfs/).​

 Can you run

 /mkbrainmask-sess//-debug -s FS_T1_501 //-fsd bold/  |& tee dng.log

 and send me dng.log ?

 doug

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

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