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Commit 152f461

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Clark
committed
General cleanup
1 parent 1e0e16a commit 152f461

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4 files changed

+32
-21
lines changed

4 files changed

+32
-21
lines changed

nipype/interfaces/fsl/dti.py

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -583,10 +583,10 @@ class ProbTrackX(FSLCommand):
583583
>>> from nipype.interfaces import fsl
584584
>>> pbx = fsl.ProbTrackX(samples_base_name='merged', mask='mask.nii', \
585585
seed='MASK_average_thal_right.nii', mode='seedmask', \
586-
xfm='trans.mat', n_samples=3, n_steps=10, force_dir=True, opd=True, os2t=True, \
587-
target_masks = ['targets_MASK1.nii', 'targets_MASK2.nii'], \
588-
thsamples='merged_thsamples.nii', fsamples='merged_fsamples.nii', phsamples='merged_phsamples.nii', \
589-
out_dir='.')
586+
xfm='trans.mat', n_samples=3, n_steps=10, force_dir=True, opd=True, \
587+
os2t=True, target_masks = ['targets_MASK1.nii', 'targets_MASK2.nii'], \
588+
thsamples='merged_thsamples.nii', fsamples='merged_fsamples.nii', \
589+
phsamples='merged_phsamples.nii', out_dir='.')
590590
>>> pbx.cmdline
591591
'probtrackx --forcedir -m mask.nii --mode=seedmask --nsamples=3 --nsteps=10 --opd --os2t --dir=. --samples=merged --seed=MASK_average_thal_right.nii --targetmasks=targets.txt --xfm=trans.mat'
592592

nipype/interfaces/fsl/model.py

Lines changed: 9 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -356,7 +356,8 @@ def _list_outputs(self):
356356
basis_key = list(self.inputs.bases.keys())[0]
357357
if basis_key in ['dgamma', 'gamma']:
358358
usetd = int(self.inputs.bases[basis_key]['derivs'])
359-
for runno, runinfo in enumerate(self._format_session_info(self.inputs.session_info)):
359+
for runno, runinfo in enumerate(
360+
self._format_session_info(self.inputs.session_info)):
360361
outputs['fsf_files'].append(os.path.join(cwd, 'run%d.fsf' % runno))
361362
outputs['ev_files'].insert(runno, [])
362363
evname = []
@@ -1258,7 +1259,8 @@ class MultipleRegressDesign(BaseInterface):
12581259
.. note::
12591260
FSL does not demean columns for higher level analysis.
12601261
1261-
Please see `FSL documentation <http://www.fmrib.ox.ac.uk/fsl/feat5/detail.html#higher>`_
1262+
Please see `FSL documentation
1263+
<http://www.fmrib.ox.ac.uk/fsl/feat5/detail.html#higher>`_
12621264
for more details on model specification for higher level analysis.
12631265
12641266
Examples
@@ -1652,10 +1654,11 @@ class ClusterInputSpec(FSLCommandInputSpec):
16521654
argstr='--omean=%s',
16531655
desc='filename for output of mean image',
16541656
hash_files=False)
1655-
out_pval_file = traits.Either(traits.Bool, File,
1656-
argstr='--opvals=%s',
1657-
desc='filename for image output of log pvals',
1658-
hash_files=False)
1657+
out_pval_file = traits.Either(
1658+
traits.Bool, File,
1659+
argstr='--opvals=%s',
1660+
desc='filename for image output of log pvals',
1661+
hash_files=False)
16591662
pthreshold = traits.Float(argstr='--pthresh=%.10f',
16601663
requires=['dlh', 'volume'],
16611664
desc='p-threshold for clusters')

nipype/interfaces/fsl/preprocess.py

Lines changed: 9 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -863,10 +863,11 @@ class FNIRTInputSpec(FSLCommandInputSpec):
863863
argstr='--refderiv',
864864
desc=('If true, ref image is used to calculate derivatives. '
865865
'Default false'))
866-
intensity_mapping_model = traits.Enum('none', 'global_linear', 'global_non_linear'
867-
'local_linear', 'global_non_linear_with_bias',
868-
'local_non_linear', argstr='--intmod=%s',
869-
desc='Model for intensity-mapping')
866+
intensity_mapping_model = traits.Enum(
867+
'none', 'global_linear', 'global_non_linear'
868+
'local_linear', 'global_non_linear_with_bias',
869+
'local_non_linear', argstr='--intmod=%s',
870+
desc='Model for intensity-mapping')
870871
intensity_mapping_order = traits.Int(
871872
argstr='--intorder=%d',
872873
desc='Order of poynomial for mapping intensities, default 5')
@@ -1330,10 +1331,12 @@ class FUGUE(FSLCommand):
13301331
a set of tools for EPI distortion correction.
13311332
13321333
Distortions may be corrected for
1333-
1. improving registration with non-distorted images (e.g. structurals), or
1334+
1. improving registration with non-distorted images (e.g. structurals),
1335+
or
13341336
2. dealing with motion-dependent changes.
13351337
1336-
FUGUE is designed to deal only with the first case - improving registration.
1338+
FUGUE is designed to deal only with the first case -
1339+
improving registration.
13371340
13381341
13391342
Examples

nipype/interfaces/fsl/utils.py

Lines changed: 10 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -682,7 +682,8 @@ def _run_interface(self, runtime):
682682
out = expr.search(runtime.stdout).groupdict()
683683
outputs = {}
684684
outputs['rotation_translation_matrix'] = [[
685-
float(v) for v in r.strip().split(' ')] for r in out['rot_tran_mat'].strip().split('\n')]
685+
float(v) for v in r.strip().split(' ')]
686+
for r in out['rot_tran_mat'].strip().split('\n')]
686687
outputs['scales'] = [
687688
float(s) for s in out['scales'].strip().split(' ')]
688689
outputs['skews'] = [float(s) for s in out['skews'].strip().split(' ')]
@@ -691,13 +692,17 @@ def _run_interface(self, runtime):
691692
outputs['left_right_orientation_preserved'] = out[
692693
'lr_orientation'].strip() == 'preserved'
693694
outputs['forward_half_transform'] = [[
694-
float(v) for v in r.strip().split(' ')] for r in out['fwd_half_xfm'].strip().split('\n')]
695+
float(v) for v in r.strip().split(' ')]
696+
for r in out['fwd_half_xfm'].strip().split('\n')]
695697
outputs['backward_half_transform'] = [[
696-
float(v) for v in r.strip().split(' ')] for r in out['bwd_half_xfm'].strip().split('\n')]
698+
float(v) for v in r.strip().split(' ')]
699+
for r in out['bwd_half_xfm'].strip().split('\n')]
697700

698701
if self.inputs.all_param:
699-
outputs['rot_angles'] = [float(r) for r in out['rot_angles'].strip().split(' ')]
700-
outputs['translations'] = [float(r) for r in out['translations'].strip().split(' ')]
702+
outputs['rot_angles'] = [
703+
float(r) for r in out['rot_angles'].strip().split(' ')]
704+
outputs['translations'] = [
705+
float(r) for r in out['translations'].strip().split(' ')]
701706

702707
setattr(self, '_results', outputs)
703708
return runtime

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