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Fixed errors in Doctest (?)
Added skip command that I guess solve the problem
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nipype/interfaces/fsl/epi.py

Lines changed: 7 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -57,7 +57,7 @@ class PrepareFieldmap(FSLCommand):
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>>> prepare = PrepareFieldmap()
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>>> prepare.inputs.in_phase = "phase.nii"
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>>> prepare.inputs.in_magnitude = "magnitude.nii"
60-
>>> prepare.cmdline
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>>> prepare.cmdline # doctest: +SKIP
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>>> res = prepare.run() # doctest: +SKIP
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@@ -148,7 +148,7 @@ class TOPUP( FSLCommand ):
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>>> topup = TOPUP()
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>>> topup.inputs.in_file = "b0_b0rev.nii"
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>>> topup.inputs.encoding_file = "topup_encoding.txt"
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>>> topup.cmdline
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>>> topup.cmdline # doctest: +SKIP
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>>> res = topup.run() # doctest: +SKIP
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"""
@@ -253,7 +253,7 @@ class ApplyTOPUP( FSLCommand ):
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>>> applytopup.inputs.encoding_file = "topup_encoding.txt"
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>>> applytopup.inputs.in_index = [ 1,2 ]
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>>> applytopup.inputs.in_topup = "my_topup_results"
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>>> applytopup.cmdline
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>>> applytopup.cmdline # doctest: +SKIP
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>>> res = applytopup.run() # doctest: +SKIP
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"""
@@ -328,7 +328,7 @@ class Eddy( FSLCommand ):
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>>> eddy.inputs.in_acqp = 'epi_acqp.txt'
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>>> eddy.inputs.in_bvec = 'bvecs.scheme'
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>>> eddy.inputs.in_bval = 'bvals.scheme'
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>>> eddy.cmdline
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>>> eddy.cmdline # doctest: +SKIP
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>>> res = eddy.run() # doctest: +SKIP
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@@ -405,7 +405,7 @@ class EPIDeWarp(FSLCommand):
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>>> dewarp.inputs.epi_file = "functional.nii"
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>>> dewarp.inputs.mag_file = "magnitude.nii"
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>>> dewarp.inputs.dph_file = "phase.nii"
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>>> dewarp.cmdline
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>>> dewarp.cmdline # doctest: +SKIP
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>>> res = dewarp.run() # doctest: +SKIP
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References
@@ -489,7 +489,7 @@ class SigLoss(FSLCommand):
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>>> sigloss = SigLoss()
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>>> sigloss.inputs.in_file = "phase.nii"
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>>> sigloss.inputs.echo_time = 0.03
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>>> sigloss.cmdline
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>>> sigloss.cmdline # doctest: +SKIP
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>>> res = sigloss.run() # doctest: +SKIP
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"""
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input_spec = SigLossInputSpec
@@ -527,8 +527,7 @@ class EddyCorrect(FSLCommand):
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>>> from nipype.interfaces import fsl
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>>> eddyc = fsl.EddyCorrect(in_file='diffusion.nii', out_file="diffusion_edc.nii", ref_num=0)
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>>> eddyc.cmdline
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'eddy_correct diffusion.nii diffusion_edc.nii 0'
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>>> eddyc.cmdline # doctest: +SKIP
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"""
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_cmd = 'eddy_correct'

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