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Interfaces for fnirtfileutils and convertwarp (FSL) #861

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Merged
merged 13 commits into from
Jul 28, 2014

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oesteban
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New interface to this two simple utilities to manage displacement fields and coefficients fields.

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Coverage increased (+0.04%) when pulling f8b4fc7 on oesteban:enh/AddInterfaceFSLWarpUtils into 7a0633c on nipy:master.

@oesteban oesteban changed the title Interface for fnirtfileutils (FSL) Interfaces for fnirtfileutils and convertwarp (FSL) Jun 18, 2014
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Coverage increased (+0.08%) when pulling 774383d on oesteban:enh/AddInterfaceFSLWarpUtils into 7a0633c on nipy:master.


if self.inputs.write_jacobian:
if not isdefined(self.inputs.out_jacobian):
self.inputs.out_jacobian = self._gen_fname(self.inputs.in_file,
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we should never modify inputs.

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Ok, but how to deal with files which name should be automatically generated but only if there's a boolean trait set? (I ask this because I honestly don't know how to do it, sorry for my ignorance).

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Ok, I think I got a solution :)

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Coverage increased (+0.08%) when pulling cee96ff on oesteban:enh/AddInterfaceFSLWarpUtils into 7a0633c on nipy:master.

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Coverage Status

Coverage increased (+0.08%) when pulling e67ed98 on oesteban:enh/AddInterfaceFSLWarpUtils into 7a0633c on nipy:master.

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Coverage Status

Coverage increased (+0.06%) when pulling 7d05c7e on oesteban:enh/AddInterfaceFSLWarpUtils into 7a0633c on nipy:master.

@chrisgorgo
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@juhuntenburg could you have a look at this? thanks!

'coordinates in the next space.'))

out_abswarp = traits.Bool(argstr='--absout', xor=['out_relwarp'],
desc=('If set it indicates that the warps in --out should be relative, i.e. '
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in line 1629 it should say 'absolute' not 'relative'

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convertwarp generally looks great, just a few things:

  • the order of concatenation should be in the arguments description, like in the original FSL help (e.g. 'applied first' for the shiftmap, as it is applied before even the premat)
  • the midmat argument would be easy and great to have too
  • and the little absolute / relative confusion (see above)

@oesteban
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With the updates from @juhuntenburg this can be merged. Thanks.

oesteban added a commit that referenced this pull request Jul 28, 2014
Interfaces for fnirtfileutils and convertwarp (FSL)
@oesteban oesteban merged commit bf7938e into nipy:master Jul 28, 2014
@oesteban oesteban deleted the enh/AddInterfaceFSLWarpUtils branch July 28, 2014 12:09
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Coverage increased (+0.07%) when pulling b065c71 on oesteban:enh/AddInterfaceFSLWarpUtils into 48bf276 on nipy:master.

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5 participants