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Update model.py
The base name tbss in randomise is very confusing, so I changed it to randomise (and removed the _, as FSL adds it too). Also, the cluster thresholds with 2 digits are not read. Not sure about the other thresholds, so I didn't touch those.
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nipype/interfaces/fsl/model.py

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -1819,7 +1819,7 @@ class RandomiseInputSpec(FSLCommandInputSpec):
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in_file = File(exists=True, desc='4D input file', argstr='-i %s',
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position=0, mandatory=True)
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base_name = traits.Str(
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'tbss_', desc='the rootname that all generated files will have',
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'randomise', desc='the rootname that all generated files will have',
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argstr='-o "%s"', position=1, usedefault=True)
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design_mat = File(
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exists=True, desc='design matrix file', argstr='-d %s', position=2)
@@ -1866,9 +1866,9 @@ class RandomiseInputSpec(FSLCommandInputSpec):
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var_smooth = traits.Int(
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argstr='-v %d', desc='use variance smoothing (std is in mm)')
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c_thresh = traits.Float(
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argstr='-c %.2f', desc='carry out cluster-based thresholding')
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argstr='-c %.1f', desc='carry out cluster-based thresholding')
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cm_thresh = traits.Float(
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argstr='-C %.2f', desc='carry out cluster-mass-based thresholding')
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argstr='-C %.1f', desc='carry out cluster-mass-based thresholding')
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f_c_thresh = traits.Float(
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argstr='-F %.2f', desc='carry out f cluster thresholding')
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f_cm_thresh = traits.Float(
@@ -1912,7 +1912,7 @@ class Randomise(FSLCommand):
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>>> import nipype.interfaces.fsl as fsl
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>>> rand = fsl.Randomise(in_file='allFA.nii', mask = 'mask.nii', tcon='design.con', design_mat='design.mat')
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>>> rand.cmdline # doctest: +ALLOW_UNICODE
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'randomise -i allFA.nii -o "tbss_" -d design.mat -t design.con -m mask.nii'
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'randomise -i allFA.nii -o "randomise" -d design.mat -t design.con -m mask.nii'
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"""
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