On Fri, Sep 18, 2009 at 2:29 AM, Mark Jenkinson <[log in to unmask]> wrote:
> Dear Nate,
>
> I was explaining why we took our original decision when
> switching from Analyze to Analyze/Nifti. At this point it is
> really quite embedded in how things work and in our libraries
> so it would require a huge effort for us and so we are not going
> to make these changes - sorry.
Bummer. Couldn't hurt to ask, though ;-)
> I would have thought that you only need to keep up one
> wrapper script - something that took in the fsl command line
> and then either determined the output type itself or had this
> passed to it as one of the arguments: e.g.
> fslstarterscript NIFTI_PAIR bet in.img out.img
> fslstarterscript NIFTI_GZ bet in.img out.nii.gz
> where fslstarterscript just did:
> export FSLOUTPUTTYPE=$1
> shift
> $@
Ah, I was thinking of doing something more elegant, to detect the
desired output from the requested filename and set the variable based
on that... then, however, you've gotta understand the command-line
parameters, so it's probably one wrapper per script. And as options
may change as new versions are released... gah. It's a Project*.
Anyhow, the easy workaround is tell people "FSL writes only .nii
files. If you want something else, convert the files post-hoc."
Pipeline, like all neuroimaging analysis software, Works The Way It
Works. The hope is that it can help us abstract the mechanical
differences between running bet and 3dSkullStrip, and let our
researchers concentrate on the scientific differences. Trick is, the
mechanical differences are pretty pervasive :(
Thanks for the info!
-Nate
* For an advanced exercise, consider a script to handle the case in
which you request that two output files have different formats ;-)
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