workflow for reconstructing tractography from dmri data

Author: baothien

examples/dmri_tractography.py

@@ -0,0 +1,74 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Thu May 16 20:39:00 2013
+
+@author: bao
+"""
+import os
+import nipype.interfaces.utility as util
+import nipype.pipeline.engine as pe
+
+from nipype.interfaces import fsl
+from nipype.workflows.dmri.fsl.dti import create_eddy_correct_pipeline
+
+from dmri_classInterfaces import BrainExtraction, EddyCorrection, ResampleVoxelSize, TensorModel, Tracking
+ 
+path ='/home/bao/tiensy/Nipype_tutorial/data/dmri/temp6/'
+data = path+ 'raw.nii.gz'
+                                        
+###### WORKFLOW DEFINITION #######
+wf=pe.Workflow(name="reconstructing_tractography")
+wf.base_dir= path + 'results'
+wf.config['execution'] = {'remove_unnecessary_outputs': 'False',
+                            }
+
+
+###### NODE DEFINITION #######
+brain_extraction_node = pe.Node(fsl.BET(), name="brain_extraction_node")
+eddy_current_correction_node = create_eddy_correct_pipeline("nipype_eddycorrect_wkf")
+resample_voxel_size_node = pe.Node(ResampleVoxelSize(), name='resample_voxel_size_node')
+tensor_model_node = pe.Node(TensorModel(), name='tensor_model_node')
+tracking_node = pe.Node(Tracking(), name='tracking_node')
+
+
+###### INPUT NODE DEFINITION #######
+#inputs: brain_extraction_node
+brain_extraction_node.inputs.in_file=data
+brain_extraction_node.inputs.frac = 0.2
+brain_extraction_node.inputs.functional = True
+#brain_extraction_node.inputs.robust = True
+brain_extraction_node.inputs.vertical_gradient = 0
+brain_extraction_node.inputs.out_file = path + 'raw_bet.nii.gz'
+
+
+#inputs: eddy_current_correction_node
+#eddy_current_correction_node.inputs.inputnode.in_file = path + 'raw_bet.nii.gz'
+eddy_current_correction_node.inputs.inputnode.ref_num = 0
+
+#inputs: resample_voxel_size_node
+resample_voxel_size_node.inputs.output_filename = path + 'data_bet_ecc_iso.nii.gz'
+
+
+#inputs: tensor_model_node
+tensor_model_node.inputs.input_filename_bvecs = path + 'raw.bvec'
+tensor_model_node.inputs.input_filename_bvals = path + 'raw.bval'
+
+tensor_model_node.inputs.output_filename_fa = path + 'tensor_fa.nii.gz'
+tensor_model_node.inputs.output_filename_evecs = path + 'tensor_evecs.nii.gz'
+
+#inputs: tracking_node
+tracking_node.inputs.num_seeds = 1000
+tracking_node.inputs.low_thresh = 0.2
+tracking_node.inputs.output_filename = path + 'dti_tracks.dpy'
+
+###### NODE CONNECTIONS #######
+wf.connect(brain_extraction_node,'out_file', eddy_current_correction_node, 'inputnode.in_file')
+wf.connect(eddy_current_correction_node,'outputnode.eddy_corrected', resample_voxel_size_node ,'input_filename')
+wf.connect(resample_voxel_size_node,'resample_file',tensor_model_node ,'input_filename_data')
+wf.connect(tensor_model_node, 'tensor_fa_file', tracking_node,'input_filename_fa')
+wf.connect(tensor_model_node, 'tensor_evecs_file', tracking_node , 'input_filename_evecs')
+
+
+###### GRAPH and RUN #######
+wf.write_graph()
+wf.run()