fix: conflicts

Author: satra

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)
 * STY: Cleanup of PEP8 violations (https://github.com/nipy/nipype/pull/2358)
 * STY: Cleanup of trailing spaces and adding of missing newlines at end of files (https://github.com/nipy/nipype/pull/2355)

nipype/interfaces/fsl/model.py

@@ -2111,11 +2111,8 @@ class RandomiseInputSpec(FSLCommandInputSpec):
         position=0,
         mandatory=True)
     base_name = traits.Str(
-        'tbss_',
-        desc='the rootname that all generated files will have',
-        argstr='-o "%s"',
-        position=1,
-        usedefault=True)
+        '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)
     tcon = File(
@@ -2161,9 +2158,9 @@ 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(
@@ -2203,7 +2200,7 @@ 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'
 
     """
 

nipype/interfaces/fsl/tests/test_auto_Randomise.py

@@ -4,63 +4,79 @@
 
 
 def test_Randomise_inputs():
-    input_map = dict(
-        args=dict(argstr='%s', ),
-        base_name=dict(
-            argstr='-o "%s"',
-            position=1,
-            usedefault=True,
-        ),
-        c_thresh=dict(argstr='-c %.2f', ),
-        cm_thresh=dict(argstr='-C %.2f', ),
-        demean=dict(argstr='-D', ),
-        design_mat=dict(
-            argstr='-d %s',
-            position=2,
-        ),
-        environ=dict(
-            nohash=True,
-            usedefault=True,
-        ),
-        f_c_thresh=dict(argstr='-F %.2f', ),
-        f_cm_thresh=dict(argstr='-S %.2f', ),
-        f_only=dict(argstr='--f_only', ),
-        fcon=dict(argstr='-f %s', ),
-        ignore_exception=dict(
-            deprecated='1.0.0',
-            nohash=True,
-            usedefault=True,
-        ),
-        in_file=dict(
-            argstr='-i %s',
-            mandatory=True,
-            position=0,
-        ),
-        mask=dict(argstr='-m %s', ),
-        num_perm=dict(argstr='-n %d', ),
-        one_sample_group_mean=dict(argstr='-1', ),
-        output_type=dict(),
-        p_vec_n_dist_files=dict(argstr='-P', ),
-        raw_stats_imgs=dict(argstr='-R', ),
-        seed=dict(argstr='--seed=%d', ),
-        show_info_parallel_mode=dict(argstr='-Q', ),
-        show_total_perms=dict(argstr='-q', ),
-        tcon=dict(
-            argstr='-t %s',
-            position=3,
-        ),
-        terminal_output=dict(
-            deprecated='1.0.0',
-            nohash=True,
-        ),
-        tfce=dict(argstr='-T', ),
-        tfce2D=dict(argstr='--T2', ),
-        tfce_C=dict(argstr='--tfce_C=%.2f', ),
-        tfce_E=dict(argstr='--tfce_E=%.2f', ),
-        tfce_H=dict(argstr='--tfce_H=%.2f', ),
-        var_smooth=dict(argstr='-v %d', ),
-        vox_p_values=dict(argstr='-x', ),
-        x_block_labels=dict(argstr='-e %s', ),
+    input_map = dict(args=dict(argstr='%s',
+    ),
+    base_name=dict(argstr='-o "%s"',
+    position=1,
+    usedefault=True,
+    ),
+    c_thresh=dict(argstr='-c %.1f',
+    ),
+    cm_thresh=dict(argstr='-C %.1f',
+    ),
+    demean=dict(argstr='-D',
+    ),
+    design_mat=dict(argstr='-d %s',
+    position=2,
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    f_c_thresh=dict(argstr='-F %.2f',
+    ),
+    f_cm_thresh=dict(argstr='-S %.2f',
+    ),
+    f_only=dict(argstr='--f_only',
+    ),
+    fcon=dict(argstr='-f %s',
+    ),
+    ignore_exception=dict(deprecated='1.0.0',
+    nohash=True,
+    usedefault=True,
+    ),
+    in_file=dict(argstr='-i %s',
+    mandatory=True,
+    position=0,
+    ),
+    mask=dict(argstr='-m %s',
+    ),
+    num_perm=dict(argstr='-n %d',
+    ),
+    one_sample_group_mean=dict(argstr='-1',
+    ),
+    output_type=dict(),
+    p_vec_n_dist_files=dict(argstr='-P',
+    ),
+    raw_stats_imgs=dict(argstr='-R',
+    ),
+    seed=dict(argstr='--seed=%d',
+    ),
+    show_info_parallel_mode=dict(argstr='-Q',
+    ),
+    show_total_perms=dict(argstr='-q',
+    ),
+    tcon=dict(argstr='-t %s',
+    position=3,
+    ),
+    terminal_output=dict(deprecated='1.0.0',
+    nohash=True,
+    ),
+    tfce=dict(argstr='-T',
+    ),
+    tfce2D=dict(argstr='--T2',
+    ),
+    tfce_C=dict(argstr='--tfce_C=%.2f',
+    ),
+    tfce_E=dict(argstr='--tfce_E=%.2f',
+    ),
+    tfce_H=dict(argstr='--tfce_H=%.2f',
+    ),
+    var_smooth=dict(argstr='-v %d',
+    ),
+    vox_p_values=dict(argstr='-x',
+    ),
+    x_block_labels=dict(argstr='-e %s',
+    ),
     )
     inputs = Randomise.input_spec()