Home · Quickstart · Documentation · Citation · NiPy

# rsfMRI: FSL, Nipype, tCompCorr

Performs preprocessing for resting state data based on the tCompCorr method described in Behzadi et al. (2007).

Tell python where to find the appropriate functions.

    import os                                    # system functions

    import nipype.interfaces.io as nio           # Data i/o
    import nipype.pipeline.engine as pe          # pypeline engine
    import nipype.interfaces.utility as util

    #####################################################################
    # Preliminaries

    from nipype.workflows.fmri.fsl import create_resting_preproc

Set up parameters for the resting state preprocessing workflow.

    TR = 3.0
    restingflow = create_resting_preproc()
    restingflow.inputs.inputspec.num_noise_components = 6
    restingflow.inputs.inputspec.highpass_sigma = 100/(2*TR)
    restingflow.inputs.inputspec.lowpass_sigma = 12.5/(2*TR)

    # Specify the location of the data.
    data_dir = os.path.abspath('data')
    # Specify the subject directories
    subject_list = ['s1']

    infosource = pe.Node(interface=util.IdentityInterface(fields=['subject_id']),
                         name="infosource")

Here we set up iteration over all the subjects.

    infosource.iterables = ('subject_id', subject_list)

## Preprocessing pipeline nodes

Now we create a `nipype.interfaces.io.DataSource` object and fill in the information from above about the layout of our data.

    datasource = pe.Node(interface=nio.DataGrabber(infields=['subject_id'],
                                                   outfields=['func', 'struct']),
                         name = 'datasource')
    datasource.inputs.base_directory = data_dir
    datasource.inputs.template = '%s/%s.nii'

    # Map field names to individual subject runs.
    info = dict(func=[['subject_id', ['f3',]]])

    datasource.inputs.template_args = info

Store significant result-files in a special directory

    datasink = pe.Node(interface=nio.DataSink(parameterization=False),
                       name='datasink')
    datasink.inputs.base_directory = os.path.abspath('./fslresting/compcorred')

## Set up complete workflow

    def get_substitutions(subject_id):
        '''Replace output names of files with more meaningful ones
        '''
        return [('vol0000_warp_merged_detrended_regfilt_filt',
                 '%s_filtered'%subject_id),
                ('vol0000_warp_merged_tsnr_stddev_thresh',
                 '%s_noisyvoxels'%subject_id)]

    l1pipeline = pe.Workflow(name= "resting")
    l1pipeline.base_dir = os.path.abspath('./fslresting/workingdir')
    l1pipeline.connect([(infosource, datasource, [('subject_id', 'subject_id')]),
                        (datasource, restingflow, [('func', 'inputspec.func')]),
                        (infosource, datasink, [('subject_id', 'container'),
                                                (('subject_id', get_substitutions),
                                                  'substitutions')]),
                        (restingflow, datasink, [('outputspec.noise_mask_file',
                                                  '@noisefile'),
                                                  ('outputspec.filtered_file',
                                                   '@filteredfile')])
                        ])

    if __name__ == '__main__':
        l1pipeline.run()
        l1pipeline.write_graph()

Example source code

You can download `the full source code of this example`. This same script is also included in the Nipype source distribution under the `examples` directory.