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jason-wgjason-wg
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Update brainsuite.py
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‎nipype/interfaces/brainsuite.py

Lines changed: 26 additions & 32 deletions
Original file line numberDiff line numberDiff line change
@@ -13,14 +13,12 @@
1313

1414
class BseInputSpec(CommandLineInputSpec):
1515

16-
inputMRIFile = File(exists=True, mandatory=True, argstr='-i %s',
17-
desc='input MRI volume', position=0)
18-
outputMRIVolume = File(mandatory=False,
19-
desc='output brain-masked MRI volume. If'
16+
inputMRIFile = File(mandatory=True, argstr='-i %s',
17+
desc='input MRI volume')
18+
outputMRIVolume = File(desc='output brain-masked MRI volume. If'
2019
'unspecified, output file name will be auto'
2120
'generated.',
22-
argstr='-o %s', position=1, hash_files=False,
23-
genfile=True)
21+
argstr='-o %s', hash_files=False, genfile=True)
2422
diffusionConstant = traits.Float(25, usedefault=True,
2523
desc='diffusion constant', argstr='-d %f')
2624
diffusionIterations = traits.Int(3, usedefault=True,
@@ -36,7 +34,7 @@ class BseInputSpec(CommandLineInputSpec):
3634
desc='dilate final mask', argstr='-p')
3735
trim = traits.Bool(True, usedefault=True, desc='trim brainstem',
3836
argstr='--trim')
39-
outputMaskFile = File(mandatory=False, desc='save smooth brain mask',
37+
outputMaskFile = File(desc='save smooth brain mask',
4038
argstr='--mask %s', hash_files=False)
4139
outputDiffusionFilter = File(desc='diffusion filter output',
4240
argstr='--adf %s', hash_files=False)
@@ -84,15 +82,13 @@ def _list_outputs(self):
8482

8583

8684
class BfcInputSpec(CommandLineInputSpec):
87-
inputMRIFile = File(exists=True, mandatory=True,
88-
desc='input skull-stripped MRI volume',
89-
argstr='-i %s', position=0)
85+
inputMRIFile = File(mandatory=True,
86+
desc='input skull-stripped MRI volume', argstr='-i %s')
9087
inputMaskFile = File(desc='mask file', argstr='-m %s', hash_files=False)
91-
outputMRIVolume = File(mandatory=False,
92-
desc='output bias-corrected MRI volume.'
88+
outputMRIVolume = File(desc='output bias-corrected MRI volume.'
9389
'If unspecified, output file name'
9490
'will be auto generated.', argstr='-o %s',
95-
position=1, hash_files=False, genfile=True)
91+
hash_files=False, genfile=True)
9692
outputBiasField = File(desc='save bias field estimate',
9793
argstr='--bias %s', hash_files=False)
9894
outputMaskedBiasField = File(desc='save bias field estimate (masked)',
@@ -191,10 +187,8 @@ def _list_outputs(self):
191187
class PvcInputSpec(CommandLineInputSpec):
192188
inputMRIFile = File(mandatory=True, desc='MRI file', argstr='-i %s')
193189
inputMaskFile = File(desc='brain mask file', argstr='-m %s')
194-
outputLabelFile = File(
195-
mandatory=False, desc='output label file. If unspecified, output file name will be auto generated.', argstr='-o %s', genfile=True)
196-
outputTissueFractionFile = File(
197-
mandatory=False, desc='output tissue fraction file', argstr='-f %s', genfile=True)
190+
outputLabelFile = File(desc='output label file. If unspecified, output file name will be auto generated.', argstr='-o %s', genfile=True)
191+
outputTissueFractionFile = File(desc='output tissue fraction file', argstr='-f %s', genfile=True)
198192
spatialPrior = traits.Float(desc='spatial prior strength', argstr='-l %f')
199193
verbosity = traits.Int(desc='verbosity level (0 = silent)', argstr='-v %d')
200194
threeClassFlag = traits.Bool(
@@ -234,10 +228,10 @@ class CerebroInputSpec(CommandLineInputSpec):
234228
inputAtlasLabelFile = File(
235229
mandatory=True, desc='atlas labeling', argstr='--atlaslabels %s')
236230
inputBrainMaskFile = File(desc='brain mask file', argstr='-m %s')
237-
outputCerebrumMaskFile = File(
238-
mandatory=False, desc='output cerebrum mask volume. If unspecified, output file name will be auto generated.', argstr='-o %s', genfile=True)
239-
outputLabelMaskFile = File(
240-
mandatory=False, desc='output labeled hemisphere/cerebrum volume. If unspecified, output file name will be auto generated.', argstr='-l %s', genfile=True)
231+
outputCerebrumMaskFile = File(desc='output cerebrum mask volume. If unspecified, output file name will be auto generated.',
232+
argstr='-o %s', genfile=True)
233+
outputLabelMaskFile = File(desc='output labeled hemisphere/cerebrum volume. If unspecified, output file name will be auto generated.',
234+
argstr='-l %s', genfile=True)
241235
costFunction = traits.Int(2, usedefault=True, desc='0,1,2', argstr='-c %d')
242236
useCentroids = traits.Bool(
243237
desc='use centroids of data to initialize position', argstr='--centroids')
@@ -290,7 +284,7 @@ class CortexInputSpec(CommandLineInputSpec):
290284
inputHemisphereLabelFile = File(
291285
mandatory=True, desc='hemisphere / lobe label volume', argstr='-h %s')
292286
outputCerebrumMask = File(
293-
mandatory=False, desc='output structure mask. If unspecified, output file name will be auto generated.', argstr='-o %s', genfile=True)
287+
desc='output structure mask. If unspecified, output file name will be auto generated.', argstr='-o %s', genfile=True)
294288
inputTissueFractionFile = File(
295289
mandatory=True, desc='tissue fraction file (32-bit float)', argstr='-f %s')
296290
tissueFractionThreshold = traits.Float(
@@ -331,7 +325,7 @@ class ScrubmaskInputSpec(CommandLineInputSpec):
331325
inputMaskFile = File(
332326
mandatory=True, desc='input structure mask file', argstr='-i %s')
333327
outputMaskFile = File(
334-
mandatory=False, desc='output structure mask file. If unspecified, output file name will be auto generated.', argstr='-o %s', genfile=True)
328+
desc='output structure mask file. If unspecified, output file name will be auto generated.', argstr='-o %s', genfile=True)
335329
backgroundFillThreshold = traits.Int(
336330
2, usedefault=True, desc='background fill threshold', argstr='-b %d')
337331
foregroundTrimThreshold = traits.Int(
@@ -369,7 +363,7 @@ class TcaInputSpec(CommandLineInputSpec):
369363
inputMaskFile = File(
370364
mandatory=True, desc='input mask volume', argstr='-i %s')
371365
outputMaskFile = File(
372-
mandatory=False, desc='output mask volume. If unspecified, output file name will be auto generated.', argstr='-o %s', genfile=True)
366+
desc='output mask volume. If unspecified, output file name will be auto generated.', argstr='-o %s', genfile=True)
373367
minCorrectionSize = traits.Int(
374368
2500, usedefault=True, desc='maximum correction size', argstr='-m %d')
375369
maxCorrectionSize = traits.Int(
@@ -406,7 +400,7 @@ def _list_outputs(self):
406400
class DewispInputSpec(CommandLineInputSpec):
407401
inputMaskFile = File(mandatory=True, desc='input file', argstr='-i %s')
408402
outputMaskFile = File(
409-
mandatory=False, desc='output file. If unspecified, output file name will be auto generated.', argstr='-o %s', genfile=True)
403+
desc='output file. If unspecified, output file name will be auto generated.', argstr='-o %s', genfile=True)
410404
verbosity = traits.Int(desc='verbosity', argstr='-v %d')
411405
sizeThreshold = traits.Int(desc='size threshold', argstr='-t %d')
412406
maximumIterations = traits.Int(
@@ -441,7 +435,7 @@ class DfsInputSpec(CommandLineInputSpec):
441435
inputVolumeFile = File(
442436
mandatory=True, desc='input 3D volume', argstr='-i %s')
443437
outputSurfaceFile = File(
444-
mandatory=False, desc='output surface mesh file. If unspecified, output file name will be auto generated.', argstr='-o %s', genfile=True)
438+
desc='output surface mesh file. If unspecified, output file name will be auto generated.', argstr='-o %s', genfile=True)
445439
inputShadingVolume = File(
446440
desc='shade surface model with data from image volume', argstr='-c %s')
447441
smoothingIterations = traits.Int(
@@ -501,7 +495,7 @@ def _list_outputs(self):
501495
class PialmeshInputSpec(CommandLineInputSpec):
502496
inputSurfaceFile = File(mandatory=True, desc='input file', argstr='-i %s')
503497
outputSurfaceFile = File(
504-
mandatory=False, desc='output file. If unspecified, output file name will be auto generated.', argstr='-o %s', genfile=True)
498+
desc='output file. If unspecified, output file name will be auto generated.', argstr='-o %s', genfile=True)
505499
verbosity = traits.Int(desc='verbosity', argstr='-v %d')
506500
inputTissueFractionFile = File(
507501
mandatory=True, desc='floating point (32) tissue fraction image', argstr='-f %s')
@@ -562,7 +556,7 @@ class SkullfinderInputSpec(CommandLineInputSpec):
562556
inputMaskFile = File(
563557
mandatory=True, desc='A brain mask file, 8-bit image (0=non-brain, 255=brain)', argstr='-m %s')
564558
outputLabelFile = File(
565-
mandatory=False, desc='output file. If unspecified, output file name will be auto generated.', argstr='-o %s', genfile=True)
559+
desc='output file. If unspecified, output file name will be auto generated.', argstr='-o %s', genfile=True)
566560
verbosity = traits.Int(desc='verbosity', argstr='-v %d')
567561
lowerThreshold = traits.Int(
568562
desc='Lower threshold for segmentation', argstr='-l %d')
@@ -613,15 +607,15 @@ class HemisplitInputSpec(CommandLineInputSpec):
613607
inputHemisphereLabelFile = File(
614608
mandatory=True, desc='input hemisphere label volume', argstr='-l %s')
615609
outputLeftHemisphere = File(
616-
mandatory=False, desc='output surface file, left hemisphere. If unspecified, output file name will be auto generated.', argstr='--left %s', genfile=True)
610+
desc='output surface file, left hemisphere. If unspecified, output file name will be auto generated.', argstr='--left %s', genfile=True)
617611
outputRightHemisphere = File(
618-
mandatory=False, desc='output surface file, right hemisphere. If unspecified, output file name will be auto generated.', argstr='--right %s', genfile=True)
612+
desc='output surface file, right hemisphere. If unspecified, output file name will be auto generated.', argstr='--right %s', genfile=True)
619613
pialSurfaceFile = File(
620614
desc='pial surface file -- must have same geometry as input surface', argstr='-p %s')
621615
outputLeftPialHemisphere = File(
622-
mandatory=False, desc='output pial surface file, left hemisphere. If unspecified, output file name will be auto generated.', argstr='-pl %s', genfile=True)
616+
desc='output pial surface file, left hemisphere. If unspecified, output file name will be auto generated.', argstr='-pl %s', genfile=True)
623617
outputRightPialHemisphere = File(
624-
mandatory=False, desc='output pial surface file, right hemisphere. If unspecified, output file name will be auto generated.', argstr='-pr %s', genfile=True)
618+
desc='output pial surface file, right hemisphere. If unspecified, output file name will be auto generated.', argstr='-pr %s', genfile=True)
625619
verbosity = traits.Int(desc='verbosity (0 = silent)', argstr='-v %d')
626620
timer = traits.Bool(desc='timing function', argstr='--timer')
627621

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