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Commit df34d2f

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Fixed tests.
1 parent 331d9e2 commit df34d2f

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3 files changed

+12
-3
lines changed

3 files changed

+12
-3
lines changed

nipype/interfaces/fsl/epi.py

Lines changed: 2 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -233,6 +233,7 @@ 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.inputs.output_type = "NIFTI_GZ"
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>>> topup.cmdline #doctest: +ELLIPSIS
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'topup --config=b02b0.cnf --datain=topup_encoding.txt \
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--imain=b0_b0rev.nii --out=b0_b0rev_base --iout=b0_b0rev_corrected.nii.gz \
@@ -354,6 +355,7 @@ class ApplyTOPUP(FSLCommand):
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>>> applytopup.inputs.in_index = [1,2]
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>>> applytopup.inputs.in_topup_fieldcoef = "topup_fieldcoef.nii.gz"
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>>> applytopup.inputs.in_topup_movpar = "topup_movpar.txt"
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>>> applytopup.inputs.output_type = "NIFTI_GZ"
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>>> applytopup.cmdline #doctest: +ELLIPSIS
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'applytopup --datain=topup_encoding.txt --imain=epi.nii,epi_rev.nii \
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--inindex=1,2 --topup=topup --out=epi_corrected.nii.gz'

nipype/interfaces/fsl/preprocess.py

Lines changed: 7 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -532,10 +532,11 @@ class FLIRT(FSLCommand):
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>>> from nipype.interfaces import fsl
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>>> from nipype.testing import example_data
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>>> flt = fsl.FLIRT(bins=640, cost_func='mutualinfo')
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>>> flt.inputs.in_file = example_data('structural.nii')
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>>> flt.inputs.reference = example_data('mni.nii')
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>>> flt.inputs.in_file = 'structural.nii'
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>>> flt.inputs.reference = 'mni.nii'
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>>> flt.inputs.output_type = "NIFTI_GZ"
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>>> flt.cmdline #doctest: +ELLIPSIS
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'flirt -in .../structural.nii -ref .../mni.nii -out structural_flirt.nii.gz -omat structural_flirt.mat -bins 640 -searchcost mutualinfo'
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'flirt -in structural.nii -ref mni.nii -out structural_flirt.nii.gz -omat structural_flirt.mat -bins 640 -searchcost mutualinfo'
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>>> res = flt.run() #doctest: +SKIP
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"""
@@ -1262,6 +1263,7 @@ class FUGUE(FSLCommand):
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>>> fugue.inputs.mask_file = 'epi_mask.nii'
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>>> fugue.inputs.shift_in_file = 'vsm.nii' # Previously computed with fugue as well
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>>> fugue.inputs.unwarp_direction = 'y'
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>>> fugue.inputs.output_type = "NIFTI_GZ"
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>>> fugue.cmdline #doctest: +ELLIPSIS
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'fugue --in=epi.nii --mask=epi_mask.nii --loadshift=vsm.nii --unwarpdir=y --unwarp=epi_unwarped.nii.gz'
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>>> fugue.run() #doctest: +SKIP
@@ -1276,6 +1278,7 @@ class FUGUE(FSLCommand):
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>>> fugue.inputs.mask_file = 'epi_mask.nii'
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>>> fugue.inputs.shift_in_file = 'vsm.nii' # Previously computed with fugue as well
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>>> fugue.inputs.unwarp_direction = 'y'
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>>> fugue.inputs.output_type = "NIFTI_GZ"
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>>> fugue.cmdline #doctest: +ELLIPSIS
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'fugue --in=epi.nii --mask=epi_mask.nii --loadshift=vsm.nii --unwarpdir=y --warp=epi_warped.nii.gz'
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>>> fugue.run() #doctest: +SKIP
@@ -1290,6 +1293,7 @@ class FUGUE(FSLCommand):
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>>> fugue.inputs.dwell_to_asym_ratio = (0.77e-3 * 3) / 2.46e-3
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>>> fugue.inputs.unwarp_direction = 'y'
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>>> fugue.inputs.save_shift = True
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>>> fugue.inputs.output_type = "NIFTI_GZ"
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>>> fugue.cmdline #doctest: +ELLIPSIS
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'fugue --dwelltoasym=0.9390243902 --mask=epi_mask.nii --phasemap=epi_phasediff.nii --saveshift=epi_phasediff_vsm.nii.gz --unwarpdir=y'
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>>> fugue.run() #doctest: +SKIP

nipype/interfaces/fsl/utils.py

Lines changed: 3 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -1359,6 +1359,7 @@ class InvWarp(FSLCommand):
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>>> invwarp = InvWarp()
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>>> invwarp.inputs.warp = "struct2mni.nii"
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>>> invwarp.inputs.reference = "anatomical.nii"
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>>> invwarp.inputs.output_type = "NIFTI_GZ"
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>>> invwarp.cmdline
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'invwarp --out=struct2mni_inverse.nii.gz --ref=anatomical.nii --warp=struct2mni.nii'
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>>> res = invwarp.run() # doctest: +SKIP
@@ -1576,6 +1577,7 @@ class WarpUtils(FSLCommand):
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>>> warputils.inputs.reference = "T1.nii"
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>>> warputils.inputs.out_format = 'spline'
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>>> warputils.inputs.warp_resolution = (10,10,10)
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>>> warputils.inputs.output_type = "NIFTI_GZ"
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>>> warputils.cmdline # doctest: +ELLIPSIS
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'fnirtfileutils --in=warpfield.nii --outformat=spline --ref=T1.nii --warpres=10.0000,10.0000,10.0000 --out=warpfield_coeffs.nii.gz'
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>>> res = invwarp.run() # doctest: +SKIP
@@ -1706,6 +1708,7 @@ class ConvertWarp(FSLCommand):
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>>> warputils.inputs.warp1 = "warpfield.nii"
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>>> warputils.inputs.reference = "T1.nii"
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>>> warputils.inputs.relwarp = True
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>>> warputils.inputs.output_type = "NIFTI_GZ"
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>>> warputils.cmdline # doctest: +ELLIPSIS
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'convertwarp --ref=T1.nii --rel --warp1=warpfield.nii --out=T1_concatwarp.nii.gz'
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>>> res = invwarp.run() # doctest: +SKIP

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