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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

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mattfeld
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@mattfeld mattfeld commented Jun 3, 2016

bedpostx expects a grad_dev.nii.gz file in subject directory if the -g flag is true.

I've tested these changes locally running a bedpostx workflow successfully on the HCP data.

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coveralls commented Jun 3, 2016

Coverage Status

Coverage decreased (-0.009%) to 72.074% when pulling cf77312 on mattfeld:master into 53cf6f8 on nipy:master.

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coveralls commented Jun 3, 2016

Coverage Status

Coverage decreased (-0.005%) to 72.078% when pulling cf77312 on mattfeld:master into 53cf6f8 on nipy:master.

@@ -348,6 +349,9 @@ def _run_interface(self, runtime):
os.path.join(subjectdir, 'bvals'))
copyfile(self.inputs.bvecs,
os.path.join(subjectdir, 'bvecs'))
_, _, ext = split_filename(self.inputs.grad_dev)
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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))

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satra commented Jun 4, 2016

thanks @mattfeld , the comment takes care of the situation when the grad_dev is not defined. also, if you could run make_specs and add the updated test_auto_bedpostx file that would be good.

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mattfeld commented Jun 6, 2016

thanks @satra for your comment. I've added the if statement for times when grad_dev is not defined, ran the make specs and updated the test_auto_BEDPOSTX5.py file. Let me know if there is anything else I need to do.

@satra satra merged commit 124a850 into nipy:master Jun 7, 2016
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3 participants