Merge remote-tracking branch 'upstream/master' into enh/spmnormalize

* upstream/master:
  fix: ensure ipython engine is not left in an undefined directory - closes #983
  Updated ApplyTransform Specs
  fixed ants ApplyTransformInputSpec
  fix error
  Enable lowb greater than zero in b0_average

Author: satra

nipype/interfaces/ants/resampling.py

@@ -249,7 +249,7 @@ class ApplyTransformsInputSpec(ANTSCommandInputSpec):
         File(exists=True), argstr='%s', mandatory=True, desc=(''))
     invert_transform_flags = InputMultiPath(traits.Bool())
     default_value = traits.Float(
-        0.0, argstr='--default-value %d', usedefault=True)
+        0.0, argstr='--default-value %g', usedefault=True)
     print_out_composite_warp_file = traits.Enum(
         0, 1, requires=["output_image"], desc=(''))  # TODO: Change to boolean
 

nipype/interfaces/ants/tests/test_auto_ApplyTransforms.py

@@ -5,7 +5,7 @@
 def test_ApplyTransforms_inputs():
     input_map = dict(args=dict(argstr='%s',
     ),
-    default_value=dict(argstr='--default-value %d',
+    default_value=dict(argstr='--default-value %g',
     usedefault=True,
     ),
     dimension=dict(argstr='--dimensionality %d',

nipype/pipeline/plugins/ipython.py

@@ -22,6 +22,8 @@ def execute_task(pckld_task, node_config, updatehash):
     from nipype import config, logging
     traceback=None
     result=None
+    import os
+    cwd = os.getcwd()
     try:
         config.update_config(node_config)
         logging.update_logging(config)
@@ -31,6 +33,7 @@ def execute_task(pckld_task, node_config, updatehash):
     except:
         traceback = format_exc()
         result = task.result
+    os.chdir(cwd)
     return result, traceback, gethostname()
 
 class IPythonPlugin(DistributedPluginBase):
@@ -72,7 +75,7 @@ def run(self, graph, config, updatehash=False):
 
     def _get_result(self, taskid):
         if taskid not in self.taskmap:
-            raise ValueError('Task %d not in pending list'%taskid)
+            raise ValueError('Task %d not in pending list' % taskid)
         if self.taskmap[taskid].ready():
             result, traceback, hostname = self.taskmap[taskid].get()
             result_out = dict(result=None, traceback=None)

nipype/workflows/dmri/fsl/utils.py

@@ -381,9 +381,11 @@ def recompose_xfm(in_bval, in_xfms):
     return out_files
 
 
-def b0_average(in_dwi, in_bval, out_file=None):
+def b0_average(in_dwi, in_bval, max_b=10.0, out_file=None):
     """
     A function that averages the *b0* volumes from a DWI dataset.
+    As current dMRI data are being acquired with all b-values > 0.0,
+    the *lowb* volumes are selected by specifying the parameter max_b.
 
     .. warning:: *b0* should be already registered (head motion artifact should
       be corrected).
@@ -403,7 +405,7 @@ def b0_average(in_dwi, in_bval, out_file=None):
     imgs = np.array(nb.four_to_three(nb.load(in_dwi)))
     bval = np.loadtxt(in_bval)
     b0s = [im.get_data().astype(np.float32)
-           for im in imgs[np.where(bval == 0)]]
+           for im in imgs[np.where(bval <= max_b)]]
     b0 = np.average(np.array(b0s), axis=0)
 
     hdr = imgs[0].get_header().copy()