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ENH Added grad_dev input to fsl.dti.bedpostx5 interface #1493

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Merged
merged 6 commits into from
Jun 7, 2016
Merged

ENH Added grad_dev input to fsl.dti.bedpostx5 interface #1493

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92538b9
Added grad_dev file to inputspec
mattfeld Sep 18, 2015
fea4dea
Added grad_dev input to BEDPOSTX5 interface
mattfeld Jun 3, 2016
6328903
changing spacing back for bedpostx5 gradnonlin inputspec
mattfeld Jun 3, 2016
cf77312
update CHANGES
mattfeld Jun 3, 2016
ed90d8a
update for when grad_dev is not defined
mattfeld Jun 6, 2016
c33d0ec
updated test_auto_BEDPOSTX5 with grad_dev input
mattfeld Jun 6, 2016
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1 change: 1 addition & 0 deletions CHANGES
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
Release 0.12.0-rc1 (April 20, 2016)
============

* ENH: Added grad_dev input to fsl.dti.bedpostx5 interface(https://github.com/nipy/nipype/pull/1493)
* ENH: ResourceMultiProc plugin to support resource allocation (https://github.com/nipy/nipype/pull/1372)
* ENH: Added dcm2niix interface (https://github.com/nipy/nipype/pull/1435)
* ENH: Add nipype_crash_search command (https://github.com/nipy/nipype/pull/1422)
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5 changes: 5 additions & 0 deletions nipype/interfaces/fsl/dti.py
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Expand Up @@ -265,6 +265,7 @@ class BEDPOSTX5InputSpec(FSLXCommandInputSpec):
usedefault=True, position=1, argstr='%s')
gradnonlin = traits.Bool(False, argstr='-g', desc=('consider gradient '
'nonlinearities, default off'))
grad_dev = File(exists=True, desc='grad_dev file, if gradnonlin, -g is True')
use_gpu = traits.Bool(False, desc='Use the GPU version of bedpostx')


Expand Down Expand Up @@ -348,6 +349,10 @@ def _run_interface(self, runtime):
os.path.join(subjectdir, 'bvals'))
copyfile(self.inputs.bvecs,
os.path.join(subjectdir, 'bvecs'))
if isdefined(self.inputs.grad_dev):
_, _, ext = split_filename(self.inputs.grad_dev)
copyfile(self.inputs.grad_dev,
os.path.join(subjectdir, 'grad_dev' + ext))

retval = super(BEDPOSTX5, self)._run_interface(runtime)

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1 change: 1 addition & 0 deletions nipype/interfaces/fsl/tests/test_auto_BEDPOSTX5.py
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Expand Up @@ -36,6 +36,7 @@ def test_BEDPOSTX5_inputs():
),
fudge=dict(argstr='-w %d',
),
grad_dev=dict(),
gradnonlin=dict(argstr='-g',
),
ignore_exception=dict(nohash=True,
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