From 410a825958222e7522bf526760b3d859952b5b05 Mon Sep 17 00:00:00 2001 From: Joke Durnez Date: Sat, 3 Jun 2017 18:00:46 -0700 Subject: [PATCH 1/3] 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. --- nipype/interfaces/fsl/model.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/nipype/interfaces/fsl/model.py b/nipype/interfaces/fsl/model.py index f45f6d62fb..d1a03a0879 100644 --- a/nipype/interfaces/fsl/model.py +++ b/nipype/interfaces/fsl/model.py @@ -1819,7 +1819,7 @@ 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) @@ -1866,9 +1866,9 @@ 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( @@ -1912,7 +1912,7 @@ 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 # doctest: +ALLOW_UNICODE - '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' """ From 3fedaabf20a75690e998067e7f5985fec33ffa6e Mon Sep 17 00:00:00 2001 From: mathiasg Date: Wed, 10 Jan 2018 16:43:08 -0500 Subject: [PATCH 2/3] fix: randomise autotest --- nipype/interfaces/fsl/tests/test_auto_Randomise.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nipype/interfaces/fsl/tests/test_auto_Randomise.py b/nipype/interfaces/fsl/tests/test_auto_Randomise.py index bcf65a0419..432455e4a8 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Randomise.py +++ b/nipype/interfaces/fsl/tests/test_auto_Randomise.py @@ -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', ), From 49323ecf1232bfceb38daed7eda4e4c3c041614a Mon Sep 17 00:00:00 2001 From: oesteban Date: Wed, 10 Jan 2018 16:43:26 -0800 Subject: [PATCH 3/3] update CHANGES --- CHANGES | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGES b/CHANGES index 01a09b735a..c69b13e672 100644 --- a/CHANGES +++ b/CHANGES @@ -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)