Thanks also for your suggestions, Matthew! This is much appreciated!
After Christina's remark I ran tbss_3 on a different cluster - it finished without error!
Thanks a lot for all your quick & constructive help!
Cheers,
Stephanie
-----Ursprüngliche Nachricht-----
Von: FSL - FMRIB's Software Library [mailto:[log in to unmask]] Im Auftrag von Matthew Webster
Gesendet: Donnerstag, 13. Dezember 2018 11:50
An: [log in to unmask]
Betreff: Re: [FSL] [FSL] tbss_3 error
Hello,
If the file mean_FA_mask ( with any image extension ) does not exist in the output folder, can you try manually re-running the command
$FSLDIR/bin/fslmaths all_FA –max 0 –Tmin –bin mean_FA_mask –odt char
and see if it gives the same error?
Kind Regards
Matthew
-------------------------------
Dr Matthew Webster
FMRIB Centre
John Radcliffe Hospital
University of Oxford
> On 13 Dec 2018, at 15:54, [log in to unmask] wrote:
>
> Thanks for your reply, Christina!
> It manages to create all_FA.nii.gz but that’s it. Disk space wise we should have more than enough space.
>
> It did run all tbss steps before but when I realized that tbss_2_reg
> had done an awful job with many of the subjects, I went back and used
> fslreorient2std and then ran everything again. This is when this error
> occurred…
>
> Von: FSL - FMRIB's Software Library [mailto:[log in to unmask]] Im
> Auftrag von Chr. Rossmanith
> Gesendet: Donnerstag, 13. Dezember 2018 10:45
> An: [log in to unmask]
> Betreff: Re: [FSL] tbss_3 error
>
> But mean_FA_mask.nii.gz has been created? What about the free disk space?
>
> Christina
>
> On 13.12.18 16:17, [log in to unmask] wrote:
> Hi FSL experts,
>
> Tbss_3_postreg –S fails with the error
>
> “$FSLDIR/bin/fslmaths all_FA –max 0 –Tmin –bin mean_FA_mask –odt char
> Image Exception: #22 :: ERROR: Could not open image mean_FA Terminate
> call after thwoing an instance of ‘RBD_COMMON::BaseException’”
>
> I ran tbss_3 again. Same error.
>
> Any idea why that is or what I could do to fix it?
>
> Thanks,
> Steph
>
> --------------------------------------------------------
>
> Stephanie Winkelbeiner, MSc, PhD student
>
> University Hospital of Psychiatry and Psychotherapy Division of
> Systems Neuroscience of Psychopathology Translational Research Center
> Bolligenstrasse 111
> 3000 Bern, Switzerland
> Phone: +41 (0)31 932 87 07
> Email: [log in to unmask]
>
>
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