Add missing option apply_isoxfm to FSL Flirt wrapper

[mick-d]

Before creating the function IsotropicReslicer, would it be possible to merge this quick fix which add the missing option apply_isoxfm to FSL Flirt wrapper?

[satra]

do we know if apply_xfm and apply_isoxfm can be used concurrently? if not we should add some xor metadata.

[mick-d]

Very good point, they cannot be used concurrently. Do you have an example
of xor metadata that I could adapt to this case?
On Jul 8, 2013 4:54 PM, "Satrajit Ghosh" notifications@github.com wrote:

In nipype/interfaces/fsl/preprocess.py:

@@ -403,6 +403,8 @@ class FLIRTInputSpec(FSLCommandInputSpec):
in_matrix_file = File(argstr='-init %s', desc='input 4x4 affine matrix')
apply_xfm = traits.Bool(argstr='-applyxfm', requires=['in_matrix_file'],
desc='apply transformation supplied by in_matrix_file')

• apply_isoxfm = traits.Float(argstr='-applyisoxfm %f',

do we know if apply_xfm and apply_isoxfm can be used concurrently? if not
we should add some xor metadata.

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Reply to this email directly or view it on GitHubhttps://github.com//pull/605/files#r5075896
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[satra]

https://github.com/nipy/nipype/blob/master/nipype/interfaces/fsl/preprocess.py#L793

[mick-d]

Sorry for the delay, no matter how small the change i wanted to test it and for some reason the latest NiPype build wanted a few more packages (dipy, nipy, etc.) which gave me some troubles

[chrisgorgo]

Please include the command line and error message.
On 9 Jul 2013 17:05, "Michael" notifications@github.com wrote:

Sorry for the delay, no matter how small the change i wanted to test it
and for some reason the latest NiPype build wanted a few more packages
(dipy, nipy, etc.) which gave me some troubles

—
Reply to this email directly or view it on GitHubhttps://github.com//pull/605#issuecomment-20680353
.

[mick-d]

It complained a lot about other packages missing, etc but in the end i could install all the dependencies. The only remaining issue is that despite having now dipy installed, i get a warning complaining about it not being installed from the tensors.py file:

lib/python2.7/site-packages/nipype/interfaces/dipy/tensors.py:26: UserWarning: dipy not installed
  warnings.warn('dipy not installed')

[mick-d]

PS: This commit works fine. The warning only appears since i installed new packages.

[mick-d]

The warning is set to be generated when dipy is not ver 0.7.0 and this is actually the case since pip install dipy provides ver 0.6.0 (not 0.7.0.) as of today. So either the warning in tensors.py should be changed to match 0.6.0 either tensors.py indeed needs dipy ver 0.7.0 and in this case the dipy pip repository would need to be updated.

[mick-d]

Any thing i should add to this PR?