Hi,
Yes, this is intentional behaviour and common across all of FSL.
The output extension (file type) is controlled by the environment variable FSLOUTPUTTYPE rather than having to be specified in each command. This makes it easier to script and for people to choose to have a blanket policy, but it does mean that it ignores the exact extension specified in the command line.
I have just read your follow-up email now and am surprised by this.
Are you exporting the FSLOUTPUTTYPE variable in the same terminal?
This really should fix it, although the NeuroDebian guys do change our install to suit their system so maybe this is something that is specific to NeuroDebian. If you can't get it to work then I would send an email to their help list.
All the best,
Mark
> On 14 Oct 2016, at 20:51, Lev E Givon <[log in to unmask]> wrote:
>
> It appears that the output file type of fslreorient2std will always be
> the same as that of the input file when no reorientation is necessary
> regardless of what one specifies on the command line. For example,
>
> fslreorient2std input.nii output.nii.gz
>
> will generate output.nii if the input doesn't need to be reoriented. Similarly,
>
> fslreorient2std input.nii.gz output.nii
>
> will generate output.nii.gz in a similar scenario. Is this behavior intentional?
>
> (I'm using FSL 5.0.9 built on Ubuntu 14.0.4.)
> --
> Lev E. Givon, PhD
> http://lebedov.github.io
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