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[FIX] Cluster threshold in randomise + change default prefix #2369

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Merged
merged 4 commits into from
Jan 11, 2018
Merged

[FIX] Cluster threshold in randomise + change default prefix #2369

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410a825
Update model.py
jokedurnez Jun 4, 2017
09465cf
fix: doctest
mgxd Jan 10, 2018
3fedaab
fix: randomise autotest
mgxd Jan 10, 2018
49323ec
update CHANGES
oesteban Jan 11, 2018
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1 change: 1 addition & 0 deletions CHANGES
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
Upcoming release (0.14.1)
================

* FIX: Cluster threshold in randomise + change default prefix (https://github.com/nipy/nipype/pull/2369)
* MAINT: Cleaning / simplify ``Node`` (https://github.com/nipy/nipype/pull/#2325)

0.14.0 (November 29, 2017)
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8 changes: 4 additions & 4 deletions nipype/interfaces/fsl/model.py
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Expand Up @@ -1887,7 +1887,7 @@ class RandomiseInputSpec(FSLCommandInputSpec):
in_file = File(exists=True, desc='4D input file', argstr='-i %s',
position=0, mandatory=True)
base_name = traits.Str(
'tbss_', desc='the rootname that all generated files will have',
'randomise', desc='the rootname that all generated files will have',
argstr='-o "%s"', position=1, usedefault=True)
design_mat = File(
exists=True, desc='design matrix file', argstr='-d %s', position=2)
Expand Down Expand Up @@ -1934,9 +1934,9 @@ class RandomiseInputSpec(FSLCommandInputSpec):
var_smooth = traits.Int(
argstr='-v %d', desc='use variance smoothing (std is in mm)')
c_thresh = traits.Float(
argstr='-c %.2f', desc='carry out cluster-based thresholding')
argstr='-c %.1f', desc='carry out cluster-based thresholding')
cm_thresh = traits.Float(
argstr='-C %.2f', desc='carry out cluster-mass-based thresholding')
argstr='-C %.1f', desc='carry out cluster-mass-based thresholding')
f_c_thresh = traits.Float(
argstr='-F %.2f', desc='carry out f cluster thresholding')
f_cm_thresh = traits.Float(
Expand Down Expand Up @@ -1980,7 +1980,7 @@ class Randomise(FSLCommand):
>>> import nipype.interfaces.fsl as fsl
>>> rand = fsl.Randomise(in_file='allFA.nii', mask = 'mask.nii', tcon='design.con', design_mat='design.mat')
>>> rand.cmdline
'randomise -i allFA.nii -o "tbss_" -d design.mat -t design.con -m mask.nii'
'randomise -i allFA.nii -o "randomise" -d design.mat -t design.con -m mask.nii'

"""

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4 changes: 2 additions & 2 deletions nipype/interfaces/fsl/tests/test_auto_Randomise.py
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Expand Up @@ -10,9 +10,9 @@ def test_Randomise_inputs():
position=1,
usedefault=True,
),
c_thresh=dict(argstr='-c %.2f',
c_thresh=dict(argstr='-c %.1f',
),
cm_thresh=dict(argstr='-C %.2f',
cm_thresh=dict(argstr='-C %.1f',
),
demean=dict(argstr='-D',
),
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