Workflow from scratch

from builtins import range

import nipype.interfaces.io as nio  # Data i/o
import nipype.interfaces.spm as spm  # spm
import nipype.pipeline.engine as pe  # pypeline engine
import nipype.algorithms.modelgen as model  # model specification
from nipype.interfaces.base import Bunch
import os  # system functions

In the following section, to showcase NiPyPe, we will describe how to create and extend a typical fMRI processing pipeline. We will begin with a basic processing layout and follow with extending it by adding/exchanging different components. Most fMRI pipeline can be divided into two sections - preprocessing and modelling. First one deals with cleaning data from confounds and noise and the second one fits a model based on the experimental design. Preprocessing stage in our first iteration of a pipeline will consist of only two steps: realignment and smoothing. In NiPyPe Every processing step consist of an Interface (which defines how to execute corresponding software) encapsulated in a Node (which defines for example a unique name). For realignment (motion correction achieved by coregistering all volumes to the mean) and smoothing (convolution with 3D Gaussian kernel) we will use SPM implementation. Definition of appropriate nodes can be found in Listing 1 (TODO). Inputs (such as register_to_mean from listing 1) of nodes are accessible through the inputs property. Upon setting any input its type is verified to avoid errors during the execution.

realign = pe.Node(interface=spm.Realign(), name="realign")
realign.inputs.register_to_mean = True

smooth = pe.Node(interface=spm.Smooth(), name="smooth")
smooth.inputs.fwhm = 4

To connect two nodes a Workflow has to be created. connect() method of a Workflow allows to specify which outputs of which Nodes should be connected to which inputs of which Nodes (see Listing 2). By connecting realigned_files output of realign to in_files input of Smooth we have created a simple preprocessing workflow (see Figure TODO).

preprocessing = pe.Workflow(name="preprocessing")
preprocessing.connect(realign, "realigned_files", smooth, "in_files")

Creating a modelling workflow which will define the design, estimate model and contrasts follows the same suite. We will again use SPM implementations. NiPyPe, however, adds extra abstraction layer to model definition which allows using the same definition for many model estimation implemantations (for example one from FSL or nippy). Therefore we will need four nodes: SpecifyModel (NiPyPe specific abstraction layer), Level1Design (SPM design definition), ModelEstimate, and ContrastEstimate. The connected modelling Workflow can be seen on Figure TODO. Model specification supports block, event and sparse designs. Contrasts provided to ContrastEstimate are defined using the same names of regressors as defined in the SpecifyModel.

specify_model = pe.Node(interface=model.SpecifyModel(), name="specify_model")
specify_model.inputs.input_units = 'secs'
specify_model.inputs.time_repetition = 3.
specify_model.inputs.high_pass_filter_cutoff = 120
specify_model.inputs.subject_info = [
    Bunch(
        conditions=['Task-Odd', 'Task-Even'],
        onsets=[list(range(15, 240, 60)),
                list(range(45, 240, 60))],
        durations=[[15], [15]])
] * 4

level1design = pe.Node(interface=spm.Level1Design(), name="level1design")
level1design.inputs.bases = {'hrf': {'derivs': [0, 0]}}
level1design.inputs.timing_units = 'secs'
level1design.inputs.interscan_interval = specify_model.inputs.time_repetition

level1estimate = pe.Node(interface=spm.EstimateModel(), name="level1estimate")
level1estimate.inputs.estimation_method = {'Classical': 1}

contrastestimate = pe.Node(
    interface=spm.EstimateContrast(), name="contrastestimate")
cont1 = ('Task>Baseline', 'T', ['Task-Odd', 'Task-Even'], [0.5, 0.5])
cont2 = ('Task-Odd>Task-Even', 'T', ['Task-Odd', 'Task-Even'], [1, -1])
contrastestimate.inputs.contrasts = [cont1, cont2]

modelling = pe.Workflow(name="modelling")
modelling.connect(specify_model, 'session_info', level1design, 'session_info')
modelling.connect(level1design, 'spm_mat_file', level1estimate, 'spm_mat_file')
modelling.connect(level1estimate, 'spm_mat_file', contrastestimate,
                  'spm_mat_file')
modelling.connect(level1estimate, 'beta_images', contrastestimate,
                  'beta_images')
modelling.connect(level1estimate, 'residual_image', contrastestimate,
                  'residual_image')

Having preprocessing and modelling workflows we need to connect them together, add data grabbing facility and save the results. For this we will create a master Workflow which will host preprocessing and model Workflows as well as DataGrabber and DataSink Nodes. NiPyPe allows connecting Nodes between Workflows. We will use this feature to connect realignment_parameters and smoothed_files to modelling workflow.

main_workflow = pe.Workflow(name="main_workflow")
main_workflow.base_dir = "workflow_from_scratch"
main_workflow.connect(preprocessing, "realign.realignment_parameters",
                      modelling, "specify_model.realignment_parameters")
main_workflow.connect(preprocessing, "smooth.smoothed_files", modelling,
                      "specify_model.functional_runs")

DataGrabber allows to define flexible search patterns which can be parameterized by user defined inputs (such as subject ID, session etc.). This allows to adapt to a wide range of file layouts. In our case we will parameterize it with subject ID. In this way we will be able to run it for different subjects. We can automate this by iterating over a list of subject Ids, by setting an iterables property on the subject_id input of DataGrabber. Its output will be connected to realignment node from preprocessing workflow.

datasource = pe.Node(
    interface=nio.DataGrabber(infields=['subject_id'], outfields=['func']),
    name='datasource')
datasource.inputs.base_directory = os.path.abspath('data')
datasource.inputs.template = '%s/%s.nii'
datasource.inputs.template_args = dict(
    func=[['subject_id', ['f3', 'f5', 'f7', 'f10']]])
datasource.inputs.subject_id = 's1'
datasource.inputs.sort_filelist = True

main_workflow.connect(datasource, 'func', preprocessing, 'realign.in_files')

DataSink on the other side provides means to storing selected results to a specified location. It supports automatic creation of folder stricter and regular expression based substitutions. In this example we will store T maps.

datasink = pe.Node(interface=nio.DataSink(), name="datasink")
datasink.inputs.base_directory = os.path.abspath(
    'workflow_from_scratch/output')

main_workflow.connect(modelling, 'contrastestimate.spmT_images', datasink,
                      '[email protected]')

main_workflow.run()
main_workflow.write_graph()

Example source code

You can download the full source code of this example. This same script is also included in Nipype1 Examples Niflow under the package/niflow/nipype1/examples directory.