5ttgen: [WARNING] FSL script 'standard_space_roi' did not complete successfully

Hi Mrtrix3 experts,

I’ve been encountering an issue with the use of the 5ttgen fsl command (5ttgen fsl T1.mif 5tt_nocoreg.mif) and was wondering if someone could provide some help. After running the above command, I receive the following error:

5ttgen: [WARNING] FSL script ‘standard_space_roi’ did not complete successfully; attempting to continue by providing un-cropped image to BET

and

5ttgen : [ERROR] Unable to find FSL output file for path “T1_BET.nii.gz”.

As I’ve never encountered this issue before I’m uncertain as to how to proceed, especially since a few days ago the command worked perfectly well and I don’t know what might have changed to prompt this.

Thank you in advance,
YP

Hi YP,

Experience has suggested that the principal source of the first warning is the unavailability of the Unix command dc, which is invoked by FSL’s standard_space_roi. If you are using MRtrix version 3.0.0 or newer, and this is indeed the case, then you should have received a warning about the absence of this command (#1908). If this is not the case, then you should interrogate the contents of the script scratch directory, specifically the log file left behind by standard_space_roi. I think that because its operation is based on registration to a template, it might be possible that that registration may go awry for some data and hence the surrounding script fails; but I still don’t have a good sense for how frequent or infrequent that might be.

Rob

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