enh: update examples with new interface

Author: mgxd

examples/fmri_ants_openfmri.py

@@ -26,7 +26,7 @@
 import nipype.pipeline.engine as pe
 import nipype.algorithms.modelgen as model
 import nipype.algorithms.rapidart as ra
-from nipype.algorithms.misc import TSNR
+from nipype.algorithms.misc import TSNR, CalculateMedian
 from nipype.interfaces.c3 import C3dAffineTool
 from nipype.interfaces import fsl, Function, ants, freesurfer as fs
 import nipype.interfaces.io as nio
@@ -55,33 +55,6 @@
     'from scipy.special import legendre'
 ]
 
-def median(in_files):
-    """Computes an average of the median of each realigned timeseries
-
-    Parameters
-    ----------
-
-    in_files: one or more realigned Nifti 4D time series
-
-    Returns
-    -------
-
-    out_file: a 3D Nifti file
-    """
-    average = None
-    for idx, filename in enumerate(filename_to_list(in_files)):
-        img = nb.load(filename, mmap=NUMPY_MMAP)
-        data = np.median(img.get_data(), axis=3)
-        if average is None:
-            average = data
-        else:
-            average = average + data
-    median_img = nb.Nifti1Image(average / float(idx + 1), img.affine,
-                                img.header)
-    filename = os.path.join(os.getcwd(), 'median.nii.gz')
-    median_img.to_filename(filename)
-    return filename
-
 
 def create_reg_workflow(name='registration'):
     """Create a FEAT preprocessing workflow together with freesurfer
@@ -818,11 +791,7 @@ def check_behav_list(behav, run_id, conds):
     wf.connect(preproc, "outputspec.realigned_files", tsnr, "in_file")
 
     # Compute the median image across runs
-    calc_median = Node(Function(input_names=['in_files'],
-                                output_names=['median_file'],
-                                function=median,
-                                imports=imports),
-                       name='median')
+    calc_median = Node(CalculateMedian(), name='median')
     wf.connect(tsnr, 'detrended_file', calc_median, 'in_files')
 
     """

examples/rsfmri_vol_surface_preprocessing.py

@@ -67,7 +67,7 @@
 # mlab.MatlabCommand.set_default_paths('/software/matlab/spm12')
 
 from nipype.algorithms.rapidart import ArtifactDetect
-from nipype.algorithms.misc import TSNR
+from nipype.algorithms.misc import TSNR, CalculateMedian
 from nipype.interfaces.utility import Rename, Merge, IdentityInterface
 from nipype.utils.filemanip import filename_to_list
 from nipype.interfaces.io import DataSink, FreeSurferSource
@@ -623,11 +623,7 @@ def create_workflow(files,
     wf.connect(slice_timing, 'timecorrected_files', tsnr, 'in_file')
 
     # Compute the median image across runs
-    calc_median = Node(Function(input_names=['in_files'],
-                                output_names=['median_file'],
-                                function=median,
-                                imports=imports),
-                       name='median')
+    calc_median = Node(CalculateMedian(), name='median')
     wf.connect(tsnr, 'detrended_file', calc_median, 'in_files')
 
     """Segment and Register

examples/rsfmri_vol_surface_preprocessing_nipy.py

@@ -65,7 +65,7 @@
 from nipype import Workflow, Node, MapNode
 
 from nipype.algorithms.rapidart import ArtifactDetect
-from nipype.algorithms.misc import TSNR
+from nipype.algorithms.misc import TSNR, CalculateMedian
 from nipype.algorithms.confounds import ACompCor
 from nipype.interfaces.utility import Rename, Merge, IdentityInterface
 from nipype.utils.filemanip import filename_to_list
@@ -556,11 +556,7 @@ def create_workflow(files,
     wf.connect(realign, "out_file", tsnr, "in_file")
 
     # Compute the median image across runs
-    calc_median = Node(Function(input_names=['in_files'],
-                                output_names=['median_file'],
-                                function=median,
-                                imports=imports),
-                       name='median')
+    calc_median = Node(CalculateMedian(), name='median')
     wf.connect(tsnr, 'detrended_file', calc_median, 'in_files')
 
     """Segment and Register