cruise_cortex_extraction¶

nighres.cortex.
cruise_cortex_extraction
(init_image, wm_image, gm_image, csf_image, vd_image=None, data_weight=0.4, regularization_weight=0.1, max_iterations=500, normalize_probabilities=False, correct_wm_pv=True, wm_dropoff_dist=1.0, topology='wcs', topology_lut_dir=None, save_data=False, overwrite=False, output_dir=None, file_name=None)[source]¶ CRUISE cortex extraction
Segments the cortex from a whole brain segmented data set with the CRUISE method (includes customized partial voluming corrections and the AnatomicallyConsistent Enhancement (ACE) of sulcal fundi).
Note that the main input images are generated by the nighres module
nighres.brain.extract_brain_region()
.Parameters:  init_image (niimg) – Initial white matter (WM) segmentation mask (binary mask>0 inside WM)
 wm_image (niimg) – Filled WM probability map (values in [0,1], including subcortical GM and ventricles)
 gm_image (niimg) – Cortical gray matter (GM) probability map (values in [0,1], highest inside the cortex)
 csf_image (niimg) – Sulcal cerebrospinal fluid (CSf) and background probability map (values in [0,1], highest in CSf and masked regions)
 vd_image (niimg, optional) – Additional probability map of vessels and dura mater to be excluded
 data_weight (float) – Weighting of probabilitybased balloon forces in CRUISE (default 0.4, sum of {data_weight,regularization_weight} should be below or equal to 1)
 regularization_weight (float) – Weighting of curvature regularization forces in CRUISE (default 0.1, sum of {data_weight,regularization_weight} should be below or equal to 1)
 max_iterations (int) – Maximum number of iterations in CRUISE (default is 500)
 normalize_probabilities (bool) – Whether to normalize the wm, gm, and csf probabilities (default is False)
 correct_wm_pv (bool) – Whether to correct for WM partial voluming in gyral crowns (default is True)
 wm_dropoff_dist (float) – Distance parameter to lower WM probabilities away from current segmentation (default is 1.0 voxel)
 topology ({'wcs', 'no'}) – Topology setting, choose ‘wcs’ (wellcomposed surfaces) for strongest topology constraint, ‘no’ for no topology constraint (default is ‘wcs’)
 topology_lut_dir (str) – Path to directory in which topology files are stored (default is stored in TOPOLOGY_LUT_DIR)
 save_data (bool) – Save output data to file (default is False)
 overwrite (bool) – Overwrite existing results (default is False)
 output_dir (str, optional) – Path to desired output directory, will be created if it doesn’t exist
 file_name (str, optional) – Desired base name for output files with file extension (suffixes will be added)
Returns: Dictionary collecting outputs under the following keys (suffix of output files in brackets)
 cortex (niimg): Hard segmentation of the cortex with labels background=0, gm=1, and wm=2 (_cruise_cortex)
 gwb (niimg): GrayWhite matter Boundary (GWB) level set function (_cruise_gwb)
 cgb (niimg): CSFGray matter Boundary (CGB) level set function (_cruise_cgb)
 avg (niimg): Central level set function, obtained as geometric average of GWB and CGB (not the middle depth of the cortex, use volumetric_layering if you want accurate depth measures) (_cruiseavg)
 thickness (niimg): Simple cortical thickness estimate: distance to the GWB and CGB surfaces, in mm (_cruisethick)
 pwm (niimg): Optimized WM probability, including partial volume and distant values correction (_cruisepwm)
 pgm (niimg): Optimized GM probability, including CSF sulcal ridges correction (_cruise_pgm)
 pcsf (niimg): Optimized CSF probability, including sulcal ridges and vessel/dura correction (_cruisepwm)
Return type: Notes
Original algorithm by Xiao Han. Java module by PierreLouis Bazin. Algorithm details can be found in [1]
References
[1] X. Han, D.L. Pham, D. Tosun, M.E. Rettmann, C. Xu, and J. L. Prince, CRUISE: Cortical Reconstruction Using Implicit Surface Evolution, NeuroImage, vol. 23, pp. 997–1012, 2004