FLIRT interface does not allow setting apply_xfm with uses_qform option

[brennerd11]

Hi all,

the FLIRT interface does not allow to set apply_xfm =True in conjunction with uses_qform=True as apply_xfm requires in_matrix_file
Anyways this should be possible as apply_xfm and uses_qform (without providing an additional matrix file) together allow resampling one image to the reference space just by utilizing the affine matrix stored in the header (see also http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FLIRT/FAQ).
I am unsure what the best way would be to fix that - just remove the required=['in_matrix_file'] from apply_xfm? Or is there a way to set require one of two inputs?

Cheers,

Daniel

[mwaskom]

There's also the nipype.fsl.ApplyXfm interface. I'm not sure if it will work better for you, but might be worth trying.

[brennerd11]

Thanks for the hint! I was not aware of that.
But unfortunately the ApplyXfm interface has the same issue - requires “in_matrix_file” when “apply_xfm” is True (default) which does not allow the comibation of only -usesqform and -applyxfm.

On 12.01.2016, at 16:05, Michael Waskom notifications@github.com wrote:

There's also the nipype.fsl.ApplyXfm http://www.mit.edu/%7Esatra/nipype-nightly/interfaces/generated/nipype.interfaces.fsl.preprocess.html#applyxfm interface. I'm not sure if it will work better for you, but might be worth trying.

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Reply to this email directly or view it on GitHub #1317 (comment).

[danella]

I am having a similar problem. I need to register my fieldmap to my EPI (using flirt or ApplyXfm) to use in FUGUE - and am unable to do it because of this glitch. Any fixes or ways around this? Thanks!

[mgxd]

@brennerd11 @danella this should be fixed in the above PR, sorry about the delay!