neurosynth/analysis/network.py
def coactivation(dataset, seed, threshold=0.0, output_dir='.', prefix='', r=6):
    """ Compute and save coactivation map given input image as seed.

    This is essentially just a wrapper for a meta-analysis defined
    by the contrast between those studies that activate within the seed
    and those that don't.

    Args:
      dataset: a Dataset instance containing study and activation data.
      seed: either a Nifti or Analyze image defining the boundaries of the
        seed, or a list of triples (x/y/z) defining the seed(s). Note that
        voxels do not need to be contiguous to define a seed--all supra-
        threshold voxels will be lumped together.
      threshold: optional float indicating the threshold above which voxels
        are considered to be part of the seed ROI (default = 0)
      r: optional integer indicating radius (in mm) of spheres to grow
        (only used if seed is a list of coordinates).
      output_dir: output directory to write to. Defaults to current.
        If none, defaults to using the first part of the seed filename.
      prefix: optional string to prepend to all coactivation images.

    Output:
      A set of meta-analysis images identical to that generated by
      meta.MetaAnalysis.
    """

    if isinstance(seed, string_types):
        ids = dataset.get_studies(mask=seed, activation_threshold=threshold)
    else:
        ids = dataset.get_studies(peaks=seed, r=r,
                                  activation_threshold=threshold)

    ma = meta.MetaAnalysis(dataset, ids)
    ma.save_results(output_dir, prefix)
def coactivation(dataset, seed, threshold=0.0, output_dir='.', prefix='', r=6):
    if isinstance(seed, string_types):
        ids = dataset.get_studies(mask=seed, activation_threshold=threshold)
    else:
        ids = dataset.get_studies(peaks=seed, r=r,
                                  activation_threshold=threshold)

    ma = meta.MetaAnalysis(dataset, ids)
    ma.save_results(output_dir, prefix)
def coactivation ( dataset , seed , threshold = 0.0 , output_dir = '.' , prefix = '' , r = 6 ) : if isinstance ( seed , string_types ) : ids = dataset . get_studies ( mask = seed , activation_threshold = threshold ) else : ids = dataset . get_studies ( peaks = seed , r = r , activation_threshold = threshold ) ma = meta . MetaAnalysis ( dataset , ids ) ma . save_results ( output_dir , prefix )
Compute and save coactivation map given input image as seed.

    This is essentially just a wrapper for a meta-analysis defined
    by the contrast between those studies that activate within the seed
    and those that don't.

    Args:
      dataset: a Dataset instance containing study and activation data.
      seed: either a Nifti or Analyze image defining the boundaries of the
        seed, or a list of triples (x/y/z) defining the seed(s). Note that
        voxels do not need to be contiguous to define a seed--all supra-
        threshold voxels will be lumped together.
      threshold: optional float indicating the threshold above which voxels
        are considered to be part of the seed ROI (default = 0)
      r: optional integer indicating radius (in mm) of spheres to grow
        (only used if seed is a list of coordinates).
      output_dir: output directory to write to. Defaults to current.
        If none, defaults to using the first part of the seed filename.
      prefix: optional string to prepend to all coactivation images.

    Output:
      A set of meta-analysis images identical to that generated by
      meta.MetaAnalysis.
Compute and save coactivation map given input image as seed .