skbold.postproc.extract_roi_info module

extract_roi_info(statfile, stat_name=None, roi_type='unilateral', per_cluster=True, cluster_engine='scipy', min_clust_size=20, stat_threshold=None, mask_threshold=20, save_indices=True, verbose=True)[source]

Extracts information per ROI for a given statistics-file. Reads in a thresholded (!) statistics-file (such as a thresholded z- or t-stat from a FSL first-level directory) and calculates for a set of ROIs the number of significant voxels included and its maximum value (+ coordinates). Saves a csv-file in the same directory as the statistics-file. Assumes that the statistics file is in MNI152 2mm space.

Parameters:
  • statfile (str) – Absolute path to statistics-file (nifti) that needs to be evaluated.
  • stat_name (str) – Name for the contrast/stat-file that is being analyzed.
  • roi_type (str) – Whether to use unilateral or bilateral masks (thus far, only Harvard- Oxford atlas masks are supported.)
  • per_cluster (bool) – Whether to evaluate the statistics-file as a whole (per_cluster=False) or per cluster separately (per_cluster=True).
  • cluster_engine (str) – Which ‘engine’ to use for clustering; can be ‘scipy’ (default), using scipy.ndimage.measurements.label, or ‘fsl’ (using FSL’s cluster commmand).
  • min_clust_size (int) – Minimum cluster size (i.e. clusters with fewer voxels than this number are discarded; also, ROIs containing fewer voxels than this will not be listed on the CSV.
  • stat_threshold (int or float) – If the stat-file contains uncorrected data, stat_threshold can be used to set a lower bound.
  • mask_threshold (bool) – Threshold for probabilistics masks, such as the Harvard-Oxford masks. Default of 25 is chosen as this minimizes overlap between adjacent masks while still covering most of the entire brain.
  • save_indices (bool) – Whether to save the indices (coordinates) of peaks of clusters.
  • verbose (bool) – Whether to print some output regarding the parsing process.
Returns:

df – Dataframe corresponding to the written csv-file.
Return type:

Dataframe