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Commit 90385cf

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author
Fabio Bernardoni
committed
changes reverted. will it pass tests now?
1 parent e8fe958 commit 90385cf

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1 file changed

+4
-71
lines changed

1 file changed

+4
-71
lines changed

‎nipype/interfaces/spm/preprocess.py‎

Lines changed: 4 additions & 71 deletions
Original file line numberDiff line numberDiff line change
@@ -204,14 +204,10 @@ class FieldMapOutputSpec(TraitedSpec):
204204

205205
class FieldMap(SPMCommand):
206206
"""Use the fieldmap toolbox from spm to calculate the voxel displacement map (VDM).
207-
208207
http://www.fil.ion.ucl.ac.uk/spm/doc/manual.pdf#page=173
209-
210208
.. important::
211-
212209
This interface does not deal with real/imag magnitude images nor
213210
with the two phase files case.
214-
215211
Examples
216212
--------
217213
>>> from nipype.interfaces.spm import FieldMap
@@ -223,7 +219,6 @@ class FieldMap(SPMCommand):
223219
>>> fm.inputs.total_readout_time = 15.6
224220
>>> fm.inputs.epi_file = 'epi.nii'
225221
>>> fm.run() # doctest: +SKIP
226-
227222
"""
228223

229224
input_spec = FieldMapInputSpec
@@ -258,13 +253,11 @@ def _list_outputs(self):
258253
class ApplyVDMInputSpec(SPMCommandInputSpec):
259254

260255
in_files = InputMultiObject(
261-
traits.Either(
262-
ImageFileSPM(exists=True), traits.List(ImageFileSPM(exists=True))
263-
),
264-
field='data.scans',
256+
ImageFileSPM(exists=True),
257+
field="data.scans",
265258
mandatory=True,
266259
copyfile=True,
267-
desc='list of filenames to apply the vdm to',
260+
desc="list of filenames to apply the vdm to",
268261
)
269262
vdmfile = File(
270263
field="data.vdmfile",
@@ -321,14 +314,10 @@ class ApplyVDMOutputSpec(TraitedSpec):
321314

322315
class ApplyVDM(SPMCommand):
323316
"""Use the fieldmap toolbox from spm to apply the voxel displacement map (VDM) to some epi files.
324-
325317
http://www.fil.ion.ucl.ac.uk/spm/doc/manual.pdf#page=173
326-
327318
.. important::
328-
329319
This interface does not deal with real/imag magnitude images nor
330320
with the two phase files case.
331-
332321
"""
333322

334323
input_spec = ApplyVDMInputSpec
@@ -339,11 +328,7 @@ class ApplyVDM(SPMCommand):
339328
def _format_arg(self, opt, spec, val):
340329
"""Convert input to appropriate format for spm"""
341330

342-
if opt == 'in_files':
343-
return scans_for_fnames(
344-
ensure_list(val), keep4d=False, separate_sessions=False
345-
)
346-
if opt == 'vdmfile':
331+
if opt in ["in_files", "vdmfile"]:
347332
return scans_for_fname(ensure_list(val))
348333
return super(ApplyVDM, self)._format_arg(opt, spec, val)
349334

@@ -435,12 +420,9 @@ class SliceTimingOutputSpec(TraitedSpec):
435420

436421
class SliceTiming(SPMCommand):
437422
"""Use spm to perform slice timing correction.
438-
439423
http://www.fil.ion.ucl.ac.uk/spm/doc/manual.pdf#page=19
440-
441424
Examples
442425
--------
443-
444426
>>> from nipype.interfaces.spm import SliceTiming
445427
>>> st = SliceTiming()
446428
>>> st.inputs.in_files = 'functional.nii'
@@ -450,7 +432,6 @@ class SliceTiming(SPMCommand):
450432
>>> st.inputs.slice_order = list(range(32,0,-1))
451433
>>> st.inputs.ref_slice = 1
452434
>>> st.run() # doctest: +SKIP
453-
454435
"""
455436

456437
input_spec = SliceTimingInputSpec
@@ -587,18 +568,14 @@ class RealignOutputSpec(TraitedSpec):
587568

588569
class Realign(SPMCommand):
589570
"""Use spm_realign for estimating within modality rigid body alignment
590-
591571
http://www.fil.ion.ucl.ac.uk/spm/doc/manual.pdf#page=25
592-
593572
Examples
594573
--------
595-
596574
>>> import nipype.interfaces.spm as spm
597575
>>> realign = spm.Realign()
598576
>>> realign.inputs.in_files = 'functional.nii'
599577
>>> realign.inputs.register_to_mean = True
600578
>>> realign.run() # doctest: +SKIP
601-
602579
"""
603580

604581
input_spec = RealignInputSpec
@@ -851,19 +828,15 @@ class RealignUnwarp(SPMCommand):
851828
of time series. Function accepts only one single field map. If in_files is a
852829
list of files they will be treated as separate sessions but associated to the
853830
same fieldmap.
854-
855831
http://www.fil.ion.ucl.ac.uk/spm/doc/manual.pdf#page=31
856-
857832
Examples
858833
--------
859-
860834
>>> import nipype.interfaces.spm as spm
861835
>>> realignUnwarp = spm.RealignUnwarp()
862836
>>> realignUnwarp.inputs.in_files = ['functional.nii', 'functional2.nii']
863837
>>> realignUnwarp.inputs.phase_map = 'voxeldisplacemap.vdm'
864838
>>> realignUnwarp.inputs.register_to_mean = True
865839
>>> realignUnwarp.run() # doctest: +SKIP
866-
867840
"""
868841

869842
input_spec = RealignUnwarpInputSpec
@@ -1028,18 +1001,14 @@ class CoregisterOutputSpec(TraitedSpec):
10281001

10291002
class Coregister(SPMCommand):
10301003
"""Use spm_coreg for estimating cross-modality rigid body alignment
1031-
10321004
http://www.fil.ion.ucl.ac.uk/spm/doc/manual.pdf#page=39
1033-
10341005
Examples
10351006
--------
1036-
10371007
>>> import nipype.interfaces.spm as spm
10381008
>>> coreg = spm.Coregister()
10391009
>>> coreg.inputs.target = 'functional.nii'
10401010
>>> coreg.inputs.source = 'structural.nii'
10411011
>>> coreg.run() # doctest: +SKIP
1042-
10431012
"""
10441013

10451014
input_spec = CoregisterInputSpec
@@ -1205,16 +1174,13 @@ class NormalizeOutputSpec(TraitedSpec):
12051174

12061175
class Normalize(SPMCommand):
12071176
"""use spm_normalise for warping an image to a template
1208-
12091177
http://www.fil.ion.ucl.ac.uk/spm/doc/manual.pdf#page=203
1210-
12111178
Examples
12121179
--------
12131180
>>> import nipype.interfaces.spm as spm
12141181
>>> norm = spm.Normalize()
12151182
>>> norm.inputs.source = 'functional.nii'
12161183
>>> norm.run() # doctest: +SKIP
1217-
12181184
"""
12191185

12201186
input_spec = NormalizeInputSpec
@@ -1437,17 +1403,14 @@ class Normalize12(SPMCommand):
14371403
known as ``New Segment`` in SPM8). Note that the normalisation in SPM12
14381404
is done towards a file containing multiple tissue probability maps, which
14391405
was not the case in SPM8.
1440-
14411406
http://www.fil.ion.ucl.ac.uk/spm/doc/manual.pdf#page=49
1442-
14431407
Examples
14441408
--------
14451409
>>> import nipype.interfaces.spm as spm
14461410
>>> norm12 = spm.Normalize12()
14471411
>>> norm12.inputs.image_to_align = 'structural.nii'
14481412
>>> norm12.inputs.apply_to_files = 'functional.nii'
14491413
>>> norm12.run() # doctest: +SKIP
1450-
14511414
"""
14521415

14531416
input_spec = Normalize12InputSpec
@@ -1679,16 +1642,13 @@ class SegmentOutputSpec(TraitedSpec):
16791642
class Segment(SPMCommand):
16801643
"""use spm_segment to separate structural images into different
16811644
tissue classes.
1682-
16831645
http://www.fil.ion.ucl.ac.uk/spm/doc/manual.pdf#page=209
1684-
16851646
Examples
16861647
--------
16871648
>>> import nipype.interfaces.spm as spm
16881649
>>> seg = spm.Segment()
16891650
>>> seg.inputs.data = 'structural.nii'
16901651
>>> seg.run() # doctest: +SKIP
1691-
16921652
"""
16931653

16941654
input_spec = SegmentInputSpec
@@ -1840,22 +1800,17 @@ class NewSegmentOutputSpec(TraitedSpec):
18401800
class NewSegment(SPMCommand):
18411801
"""Use spm_preproc8 (New Segment) to separate structural images into
18421802
different tissue classes. Supports multiple modalities.
1843-
18441803
NOTE: This interface currently supports single channel input only
1845-
18461804
http://www.fil.ion.ucl.ac.uk/spm/doc/manual.pdf#page=43
1847-
18481805
Examples
18491806
--------
18501807
>>> import nipype.interfaces.spm as spm
18511808
>>> seg = spm.NewSegment()
18521809
>>> seg.inputs.channel_files = 'structural.nii'
18531810
>>> seg.inputs.channel_info = (0.0001, 60, (True, True))
18541811
>>> seg.run() # doctest: +SKIP
1855-
18561812
For VBM pre-processing [http://www.fil.ion.ucl.ac.uk/~john/misc/VBMclass10.pdf],
18571813
TPM.nii should be replaced by /path/to/spm8/toolbox/Seg/TPM.nii
1858-
18591814
>>> seg = NewSegment()
18601815
>>> seg.inputs.channel_files = 'structural.nii'
18611816
>>> tissue1 = (('TPM.nii', 1), 2, (True,True), (False, False))
@@ -1865,7 +1820,6 @@ class NewSegment(SPMCommand):
18651820
>>> tissue5 = (('TPM.nii', 5), 2, (False,False), (False, False))
18661821
>>> seg.inputs.tissues = [tissue1, tissue2, tissue3, tissue4, tissue5]
18671822
>>> seg.run() # doctest: +SKIP
1868-
18691823
"""
18701824

18711825
input_spec = NewSegmentInputSpec
@@ -2088,19 +2042,15 @@ class MultiChannelNewSegmentOutputSpec(TraitedSpec):
20882042
class MultiChannelNewSegment(SPMCommand):
20892043
"""Use spm_preproc8 (New Segment) to separate structural images into
20902044
different tissue classes. Supports multiple modalities and multichannel inputs.
2091-
20922045
http://www.fil.ion.ucl.ac.uk/spm/doc/manual.pdf#page=45
2093-
20942046
Examples
20952047
--------
20962048
>>> import nipype.interfaces.spm as spm
20972049
>>> seg = spm.MultiChannelNewSegment()
20982050
>>> seg.inputs.channels = [('structural.nii',(0.0001, 60, (True, True)))]
20992051
>>> seg.run() # doctest: +SKIP
2100-
21012052
For VBM pre-processing [http://www.fil.ion.ucl.ac.uk/~john/misc/VBMclass10.pdf],
21022053
TPM.nii should be replaced by /path/to/spm8/toolbox/Seg/TPM.nii
2103-
21042054
>>> seg = MultiChannelNewSegment()
21052055
>>> channel1= ('T1.nii',(0.0001, 60, (True, True)))
21062056
>>> channel2= ('T2.nii',(0.0001, 60, (True, True)))
@@ -2112,7 +2062,6 @@ class MultiChannelNewSegment(SPMCommand):
21122062
>>> tissue5 = (('TPM.nii', 5), 2, (False,False), (False, False))
21132063
>>> seg.inputs.tissues = [tissue1, tissue2, tissue3, tissue4, tissue5]
21142064
>>> seg.run() # doctest: +SKIP
2115-
21162065
"""
21172066

21182067
input_spec = MultiChannelNewSegmentInputSpec
@@ -2270,9 +2219,7 @@ class SmoothOutputSpec(TraitedSpec):
22702219

22712220
class Smooth(SPMCommand):
22722221
"""Use spm_smooth for 3D Gaussian smoothing of image volumes.
2273-
22742222
http://www.fil.ion.ucl.ac.uk/spm/doc/manual.pdf#page=55
2275-
22762223
Examples
22772224
--------
22782225
>>> import nipype.interfaces.spm as spm
@@ -2345,12 +2292,10 @@ class DARTELInputSpec(SPMCommandInputSpec):
23452292
field="warp.settings.param",
23462293
desc="""\
23472294
List of tuples for each iteration
2348-
23492295
* Inner iterations
23502296
* Regularization parameters
23512297
* Time points for deformation model
23522298
* smoothing parameter
2353-
23542299
""",
23552300
)
23562301
optimization_parameters = traits.Tuple(
@@ -2360,11 +2305,9 @@ class DARTELInputSpec(SPMCommandInputSpec):
23602305
field="warp.settings.optim",
23612306
desc="""\
23622307
Optimization settings a tuple:
2363-
23642308
* LM regularization
23652309
* cycles of multigrid solver
23662310
* relaxation iterations
2367-
23682311
""",
23692312
)
23702313

@@ -2379,16 +2322,13 @@ class DARTELOutputSpec(TraitedSpec):
23792322

23802323
class DARTEL(SPMCommand):
23812324
"""Use spm DARTEL to create a template and flow fields
2382-
23832325
http://www.fil.ion.ucl.ac.uk/spm/doc/manual.pdf#page=185
2384-
23852326
Examples
23862327
--------
23872328
>>> import nipype.interfaces.spm as spm
23882329
>>> dartel = spm.DARTEL()
23892330
>>> dartel.inputs.image_files = [['rc1s1.nii','rc1s2.nii'],['rc2s1.nii', 'rc2s2.nii']]
23902331
>>> dartel.run() # doctest: +SKIP
2391-
23922332
"""
23932333

23942334
input_spec = DARTELInputSpec
@@ -2503,9 +2443,7 @@ class DARTELNorm2MNIOutputSpec(TraitedSpec):
25032443

25042444
class DARTELNorm2MNI(SPMCommand):
25052445
"""Use spm DARTEL to normalize data to MNI space
2506-
25072446
http://www.fil.ion.ucl.ac.uk/spm/doc/manual.pdf#page=188
2508-
25092447
Examples
25102448
--------
25112449
>>> import nipype.interfaces.spm as spm
@@ -2515,7 +2453,6 @@ class DARTELNorm2MNI(SPMCommand):
25152453
>>> nm.inputs.apply_to_files = ['c1s1.nii', 'c1s3.nii']
25162454
>>> nm.inputs.modulate = True
25172455
>>> nm.run() # doctest: +SKIP
2518-
25192456
"""
25202457

25212458
input_spec = DARTELNorm2MNIInputSpec
@@ -2598,17 +2535,14 @@ class CreateWarpedOutputSpec(TraitedSpec):
25982535

25992536
class CreateWarped(SPMCommand):
26002537
"""Apply a flow field estimated by DARTEL to create warped images
2601-
26022538
http://www.fil.ion.ucl.ac.uk/spm/doc/manual.pdf#page=190
2603-
26042539
Examples
26052540
--------
26062541
>>> import nipype.interfaces.spm as spm
26072542
>>> create_warped = spm.CreateWarped()
26082543
>>> create_warped.inputs.image_files = ['rc1s1.nii', 'rc1s2.nii']
26092544
>>> create_warped.inputs.flowfield_files = ['u_rc1s1_Template.nii', 'u_rc1s2_Template.nii']
26102545
>>> create_warped.run() # doctest: +SKIP
2611-
26122546
"""
26132547

26142548
input_spec = CreateWarpedInputSpec
@@ -2890,7 +2824,6 @@ class VBMSegmentOuputSpec(TraitedSpec):
28902824
class VBMSegment(SPMCommand):
28912825
"""Use VBM8 toolbox to separate structural images into different
28922826
tissue classes.
2893-
28942827
Example
28952828
-------
28962829
>>> import nipype.interfaces.spm as spm

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