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Prepare interface implemented
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-109
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2 files changed

+126
-109
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‎nipype/interfaces/fsl/__init__.py‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -15,12 +15,12 @@
1515
from .utils import (Smooth, Merge, ExtractROI, Split, ImageMaths, ImageMeants,
1616
ImageStats, FilterRegressor, Overlay, Slicer,
1717
PlotTimeSeries, PlotMotionParams, ConvertXFM,
18-
SwapDimensions, PowerSpectrum, SigLoss, Reorient2Std,
18+
SwapDimensions, PowerSpectrum, Reorient2Std,
1919
Complex, InvWarp)
2020

21-
from .epi import (EPIDewarp, SigLoss,EddyCorrect)
21+
from .epi import (PrepareFieldmap,EPIDeWarp, SigLoss,EddyCorrect)
2222

23-
from .dti import (EddyCorrect, BEDPOSTX, DTIFit, ProbTrackX, VecReg, ProjThresh,
23+
from .dti import (BEDPOSTX, DTIFit, ProbTrackX, VecReg, ProjThresh,
2424
FindTheBiggest, DistanceMap, TractSkeleton, XFibres,
2525
MakeDyadicVectors)
2626
from .maths import (ChangeDataType, Threshold, MeanImage, ApplyMask,

‎nipype/interfaces/fsl/epi.py‎

Lines changed: 123 additions & 106 deletions
Original file line numberDiff line numberDiff line change
@@ -19,6 +19,8 @@
1919
from nipype.interfaces.fsl.base import FSLCommand, FSLCommandInputSpec, Info
2020
from nipype.interfaces.base import (traits, TraitedSpec, OutputMultiPath, File,
2121
isdefined)
22+
23+
2224
from nipype.utils.filemanip import load_json, save_json, split_filename, fname_presuffix
2325

2426
warn = warnings.warn
@@ -34,14 +36,14 @@ class PrepareFieldmapInputSpec(FSLCommandInputSpec):
3436
desc='Magnitude difference map, brain extracted',
3537
mandatory=True
3638
)
37-
out_fieldmap = File()
39+
out_fieldmap = File( desc='output name for prepared fieldmap', position=3 )
3840
delta_TE = traits.Float(2.46,desc='echo time difference of the fielmap sequence in ms. (usually 2.46ms in Siemens)',
39-
usedefault=True )
41+
position=4, usedefault=True )
4042
nocheck = traits.Bool(False,desc='do not perform sanity checks for image size/range/dimensions',
41-
argstr='--nocheck' )
43+
position=5, argstr='--nocheck' )
4244

43-
class PrepareFieldmapOutputSpec( FSLCommandOutputSpec ):
44-
out_fieldmap = File( exists=True )
45+
class PrepareFieldmapOutputSpec( TraitedSpec ):
46+
out_fieldmap = File( exists=True, desc='output name for prepared fieldmap' )
4547

4648
class PrepareFieldmap(FSLCommand):
4749
""" Interface for the fsl_prepare_fielmap script
@@ -63,117 +65,132 @@ class PrepareFieldmap(FSLCommand):
6365
input_spec = PrepareFieldmapInputSpec
6466
output_spec = PrepareFieldmapOutputSpec
6567

66-
def _list_outputs(self):
67-
outputs = self.output_spec().get()
68-
69-
return outputs
70-
71-
72-
class TOPUPInputSpec( FSLCommandInputSpec ):
73-
in_file = File( exists=True, mandatory=True, desc='name of 4D file with images', argstr='--imain %s' )
74-
encoding_file = File( exists=True, mandatory=True, desc='name of text file with PE directions/times', argstr='--datain %s' )
75-
out_base = File( desc='base-name of output files (spline coefficients (Hz) and movement parameters)', argstr='--out %s' )
76-
out_field = File( argstr='--fout %s', desc='name of image file with field (Hz)' )
77-
out_corrected = File( argstr='--iout %s', desc='name of 4D image file with unwarped images' )
78-
out_logfile = File( argstr='--logout %s', desc='name of log-file' )
79-
warp_res = traits.Float( 10.0, argstr='--warpres %f', desc='(approximate) resolution (in mm) of warp basis for the different sub-sampling levels' )
80-
subsamp = traits.Int( 1, argstr='--subsamp %d', desc='sub-sampling scheme, default 1' )
81-
fwhm = traits.Float( 8.0, argstr='--fwhm %f', desc='FWHM (in mm) of gaussian smoothing kernel' )
82-
config = File( desc='Name of config file specifying command line arguments', argstr='--config %s' )
83-
max_iter = traits.Int( 5, argstr='--miter %d', desc='max # of non-linear iterations')
84-
#lambda Weight of regularisation, default depending on --ssqlambda and --regmod switches. See user documetation.
85-
#ssqlambda If set (=1), lambda is weighted by current ssq, default 1
86-
#regmod Model for regularisation of warp-field [membrane_energy bending_energy], default bending_energy
87-
estmov = traits.Either( (0,1), desc='estimate movements if set', argstr='--estmov %d' )
88-
minmet = traits.Either( (0,1), desc='Minimisation method 0=Levenberg-Marquardt, 1=Scaled Conjugate Gradient', argstr='--minmet %d' )
89-
splineorder = traits.Int( 3, argstr='--splineorder %d', desc='order of spline, 2->Qadratic spline, 3->Cubic spline' )
90-
numprec = traits.Either( ('float','double'), argstr='--numprec %s', desc='Precision for representing Hessian, double or float.' )
91-
interp = traits.Either( ('linear','spline'), argstr='--interp %s', desc='Image interpolation model, linear or spline.' )
92-
scale = traits.Either( (0,1), argstr='--scale %d', desc='If set (=1), the images are individually scaled to a common mean' )
93-
regrid = traits.Either( (0,1), argstr='--regrid %d', desc='If set (=1), the calculations are done in a different grid' )
94-
68+
def _parse_inputs( self, skip=None ):
69+
if skip is None:
70+
skip = []
71+
72+
if not isdefined(self.inputs.out_fieldmap ):
73+
self.inputs.out_fieldmap = self._gen_fname(
74+
self.inputs.in_phase, suffix='_fslprepared' )
9575

76+
if not isdefined(self.inputs.nocheck ) or not self.inputs.nocheck:
77+
skip += ['nocheck']
9678

97-
class TOPUPOutputSpec( FSLCommandOutputSpec ):
98-
out_field = File( argstr='--fout %s', desc='name of image file with field (Hz)' )
99-
out_corrected = File( argstr='--iout %s', desc='name of 4D image file with unwarped images' )
100-
out_logfile = File( argstr='--logout %s', desc='name of log-file' )
79+
return super(PrepareFieldmap, self)._parse_inputs(skip=skip)
10180

10281

103-
104-
class TOPUP( FSLCommand ):
105-
""" Interface for FSL topup, a tool for estimating and correcting susceptibility induced distortions
106-
Reference: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/TOPUP
107-
Example: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/topup/ExampleTopupFollowedByApplytopup
108-
109-
topup --imain=<some 4D image> --datain=<text file> --config=<text file with parameters> --coutname=my_field
110-
111-
112-
Examples
113-
--------
114-
>>> topup = TOPUP()
115-
>>> topup.inputs.in_file = "dwi_combined.nii"
116-
>>> topup.inputs.encoding_file = "encoding.txt"
117-
>>> res = topup.run() # doctest: +SKIP
118-
119-
"""
120-
_cmd = 'topup'
121-
input_spec = TOPUPInputSpec
122-
output_spec = TOPUPOutputSpec
123-
12482
def _list_outputs(self):
12583
outputs = self.output_spec().get()
84+
outputs['out_fieldmap'] = self.inputs.out_fieldmap
12685

12786
return outputs
12887

12988

130-
131-
class ApplyTOPUPInputSpec( FSLCommandInputSpec ):
132-
in_file = File( exists=True, mandatory=True, desc='name of 4D file with images', argstr='--imain %s' )
133-
encoding_file = File( exists=True, mandatory=True, desc='name of text file with PE directions/times', argstr='--datain %s' )
134-
in_index = traits.List( argstr='-x %s', mandatory=True, desc='comma separated list of indicies into --datain of the input image (to be corrected)' )
135-
in_topup = File( mandatory=True, desc='basename of field/movements (from topup)', argstr='-t %s' )
136-
137-
out_base = File( desc='basename for output (warped) image', argstr='-o %s' )
138-
method = traits.Either( ('jac','lsr'), argstr='-m %s', desc='use jacobian modulation (jac) or least-squares resampling (lsr)' )
139-
interp = traits.Either( ('trilinear','spline'), argstr='-n %s', desc='interpolation method' )
140-
datatype = traits.Either( ('char', 'short', 'int', 'float', 'double' ), argstr='-d %s', desc='force output data type' )
141-
142-
143-
class ApplyTOPUPOutputSpec( FSLCommandOutputSpec ):
144-
out_corrected = File( argstr='--iout %s', desc='name of 4D image file with unwarped images' )
145-
out_logfile = File( argstr='--logout %s', desc='name of log-file' )
146-
147-
class ApplyTOPUP( FSLCommand ):
148-
""" Interface for FSL topup, a tool for estimating and correcting susceptibility induced distortions
149-
Reference: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/topup/ApplytopupUsersGuide
150-
Example: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/topup/ExampleTopupFollowedByApplytopup
151-
152-
topup --imain=<some 4D image> --datain=<text file> --config=<text file with parameters> --coutname=my_field
153-
154-
155-
Examples
156-
--------
157-
>>> applytopup = ApplyTOPUP()
158-
>>> applytopup.inputs.in_file = "dwi_combined.nii"
159-
>>> applytopup.inputs.encoding_file = "encoding.txt"
160-
>>> applytopup.inputs.in_index = 1,2
161-
>>> applytopup.inputs.in_topup = "my_topup_results"
162-
>>> res = applytopup.run() # doctest: +SKIP
163-
164-
"""
165-
_cmd = 'topup'
166-
input_spec = ApplyTOPUPInputSpec
167-
output_spec = ApplyTOPUPOutputSpec
168-
169-
def _list_outputs(self):
170-
outputs = self.output_spec().get()
171-
172-
return outputs
173-
174-
175-
176-
89+
# class TOPUPInputSpec( FSLCommandInputSpec ):
90+
# in_file = File( exists=True, mandatory=True, desc='name of 4D file with images', argstr='--imain %s' )
91+
# encoding_file = File( exists=True, mandatory=True, desc='name of text file with PE directions/times', argstr='--datain %s' )
92+
# out_base = File( desc='base-name of output files (spline coefficients (Hz) and movement parameters)', argstr='--out %s' )
93+
# out_field = File( argstr='--fout %s', desc='name of image file with field (Hz)' )
94+
# out_corrected = File( argstr='--iout %s', desc='name of 4D image file with unwarped images' )
95+
# out_logfile = File( argstr='--logout %s', desc='name of log-file' )
96+
# warp_res = traits.Float( 10.0, argstr='--warpres %f', desc='(approximate) resolution (in mm) of warp basis for the different sub-sampling levels' )
97+
# subsamp = traits.Int( 1, argstr='--subsamp %d', desc='sub-sampling scheme, default 1' )
98+
# fwhm = traits.Float( 8.0, argstr='--fwhm %f', desc='FWHM (in mm) of gaussian smoothing kernel' )
99+
# config = File( desc='Name of config file specifying command line arguments', argstr='--config %s' )
100+
# max_iter = traits.Int( 5, argstr='--miter %d', desc='max # of non-linear iterations')
101+
# #lambda Weight of regularisation, default depending on --ssqlambda and --regmod switches. See user documetation.
102+
# #ssqlambda If set (=1), lambda is weighted by current ssq, default 1
103+
# #regmod Model for regularisation of warp-field [membrane_energy bending_energy], default bending_energy
104+
# estmov = traits.Either( (0,1), desc='estimate movements if set', argstr='--estmov %d' )
105+
# minmet = traits.Either( (0,1), desc='Minimisation method 0=Levenberg-Marquardt, 1=Scaled Conjugate Gradient', argstr='--minmet %d' )
106+
# splineorder = traits.Int( 3, argstr='--splineorder %d', desc='order of spline, 2->Qadratic spline, 3->Cubic spline' )
107+
# numprec = traits.Either( ('float','double'), argstr='--numprec %s', desc='Precision for representing Hessian, double or float.' )
108+
# interp = traits.Either( ('linear','spline'), argstr='--interp %s', desc='Image interpolation model, linear or spline.' )
109+
# scale = traits.Either( (0,1), argstr='--scale %d', desc='If set (=1), the images are individually scaled to a common mean' )
110+
# regrid = traits.Either( (0,1), argstr='--regrid %d', desc='If set (=1), the calculations are done in a different grid' )
111+
#
112+
#
113+
#
114+
# class TOPUPOutputSpec( TraitedSpec ):
115+
# out_field = File( argstr='--fout %s', desc='name of image file with field (Hz)' )
116+
# out_corrected = File( argstr='--iout %s', desc='name of 4D image file with unwarped images' )
117+
# out_logfile = File( argstr='--logout %s', desc='name of log-file' )
118+
#
119+
#
120+
#
121+
# class TOPUP( FSLCommand ):
122+
# """ Interface for FSL topup, a tool for estimating and correcting susceptibility induced distortions
123+
# Reference: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/TOPUP
124+
# Example: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/topup/ExampleTopupFollowedByApplytopup
125+
#
126+
# topup --imain=<some 4D image> --datain=<text file> --config=<text file with parameters> --coutname=my_field
127+
#
128+
#
129+
# Examples
130+
# --------
131+
# >>> topup = TOPUP()
132+
# >>> topup.inputs.in_file = "dwi_combined.nii"
133+
# >>> topup.inputs.encoding_file = "encoding.txt"
134+
# >>> res = topup.run() # doctest: +SKIP
135+
#
136+
# """
137+
# _cmd = 'topup'
138+
# input_spec = TOPUPInputSpec
139+
# output_spec = TOPUPOutputSpec
140+
#
141+
# def _list_outputs(self):
142+
# outputs = self.output_spec().get()
143+
#
144+
# return outputs
145+
#
146+
#
147+
#
148+
# class ApplyTOPUPInputSpec( FSLCommandInputSpec ):
149+
# in_file = File( exists=True, mandatory=True, desc='name of 4D file with images', argstr='--imain %s' )
150+
# encoding_file = File( exists=True, mandatory=True, desc='name of text file with PE directions/times', argstr='--datain %s' )
151+
# in_index = traits.List( argstr='-x %s', mandatory=True, desc='comma separated list of indicies into --datain of the input image (to be corrected)' )
152+
# in_topup = File( mandatory=True, desc='basename of field/movements (from topup)', argstr='-t %s' )
153+
#
154+
# out_base = File( desc='basename for output (warped) image', argstr='-o %s' )
155+
# method = traits.Either( ('jac','lsr'), argstr='-m %s', desc='use jacobian modulation (jac) or least-squares resampling (lsr)' )
156+
# interp = traits.Either( ('trilinear','spline'), argstr='-n %s', desc='interpolation method' )
157+
# datatype = traits.Either( ('char', 'short', 'int', 'float', 'double' ), argstr='-d %s', desc='force output data type' )
158+
#
159+
#
160+
# class ApplyTOPUPOutputSpec( TraitedSpec ):
161+
# out_corrected = File( argstr='--iout %s', desc='name of 4D image file with unwarped images' )
162+
# out_logfile = File( argstr='--logout %s', desc='name of log-file' )
163+
#
164+
# class ApplyTOPUP( FSLCommand ):
165+
# """ Interface for FSL topup, a tool for estimating and correcting susceptibility induced distortions
166+
# Reference: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/topup/ApplytopupUsersGuide
167+
# Example: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/topup/ExampleTopupFollowedByApplytopup
168+
#
169+
# topup --imain=<some 4D image> --datain=<text file> --config=<text file with parameters> --coutname=my_field
170+
#
171+
#
172+
# Examples
173+
# --------
174+
# >>> applytopup = ApplyTOPUP()
175+
# >>> applytopup.inputs.in_file = "dwi_combined.nii"
176+
# >>> applytopup.inputs.encoding_file = "encoding.txt"
177+
# >>> applytopup.inputs.in_index = 1,2
178+
# >>> applytopup.inputs.in_topup = "my_topup_results"
179+
# >>> res = applytopup.run() # doctest: +SKIP
180+
#
181+
# """
182+
# _cmd = 'topup'
183+
# input_spec = ApplyTOPUPInputSpec
184+
# output_spec = ApplyTOPUPOutputSpec
185+
#
186+
# def _list_outputs(self):
187+
# outputs = self.output_spec().get()
188+
#
189+
# return outputs
190+
#
191+
#
192+
#
193+
#
177194

178195

179196
class EPIDeWarpInputSpec(FSLCommandInputSpec):

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