simple FS example

Author: chrisgorgo

examples/amri_freesurfer.py

@@ -0,0 +1,50 @@
+import nipype.pipeline.engine as pe
+import nipype.interfaces.io as nio
+import nipype.interfaces.utility as util
+import os
+from nipype.interfaces.freesurfer.preprocess import ReconAll
+
+subject_list = ['s1', 's3']
+data_dir = os.path.abspath('data')
+subjects_dir = os.path.abspath('amri_freesurfer_tutorial/subjects_dir')
+
+wf = pe.Workflow(name="l1workflow")
+wf.base_dir = os.path.abspath('amri_freesurfer_tutorial/workdir')
+
+datasource = pe.MapNode(interface=nio.DataGrabber(infields=['subject_id'],
+ outfields=['struct']),
+ name='datasource',
+ iterfield=['subject_id'])
+datasource.inputs.base_directory = data_dir
+datasource.inputs.template = '%s/%s.nii'
+datasource.inputs.template_args = dict(struct=[['subject_id', 'struct']])
+datasource.inputs.subject_id = subject_list
+
+recon_all = pe.MapNode(interface=ReconAll(), name='recon_all',
+ iterfield=['subject_id'])
+recon_all.inputs.subject_id = subject_list
+
+wf.connect(datasource, 'struct', recon_all, 'T1_files')
+
+
+def MakeAverageSubject(subjects_dir, subjects_list, out_name):
+ from nipype.interfaces.base import CommandLine
+ mas = CommandLine(command='make_average_subject')
+ mas.inputs.args = "--sdir %s --subjects %s --out %s"%(subjects_dir, " "%subject_list, out_name)
+ mas.run()
+ return subjects_dir, out_name
+
+average = pe.Node(interface=util.Function(input_names=['subjects_dir',
+ 'subjects_list',
+ 'out_name'],
+ output_names=['subjects_dir',
+ 'out_name'],
+ function=MakeAverageSubject),
+ name="average")
+
+average.inputs.out_name = "average"
+
+wf.connect(recon_all, 'subjects_dir', average, 'subjects_dir')
+wf.connect(recon_all, 'subject_id', average, 'subjects_list')
+
+wf.run("MultiProc", plugin_args={'n_procs': 4})