gridgen

Parameters

Parameters should be saved as a json file. You can pass the parameters with the command gridgen parameters.json func where func is one of the possible functions (grid2d, ecog, fit etc). You can also use the command gridgen parameters.json parameters to generate a template parameters.json file.

• output_dir: (str, optional) path to output directory
• grid2d (required by command grid2d)
  • n_rows: (int) number of rows
  • n_columns: (int) number of columns
  • direction: (str) direction of the grid (wires are by definition at the bottom). Values: [TBLR, TBRL, BTLR, BTRL, LRTB, LRBT, RLTB, RLBT]. Default: TBLR
  • chan_pattern: (str, optional) pattern to name the channels (it should match the naming pattern of the data). Examples are “chan{}” or “chan{03d}
• ecog (required by command ecog)
  • ecog_file: (str) path to ECoG file
  • freq_range: (list) low and high threshold of the frequency range of interest. Default: [65, 95]
  • begtime: (float, optional) start time in seconds from the beginning of the file
  • endtime: (float, optional) end time in seconds from the beginning of the file
  • bad_channels: (list, optional) list of str, name of the channels to exclude
• grid3d (required by command grid3d, fit)
  • interelec_distance: (float, optional) distance between the electrode centers (pitch), in mm. Default: 3
  • maximum_angle: (float, optional) maximum angle, in degrees, that the grid can flex, between two neighboring electrodes (elasticity of the grid). Default: 5
  • step_angle: (float, optional) step size, in degrees, when computing range between -maximum_angle and +maximum_angle. The smaller the step size, the faster the generation of the grid. Default: 0.25
• mri (required by command grid3d, fit, matlab)
  • T1_file: (str) path to T1 image (in particular, the T1.mgz from freesurfer). Only used to compute the mapping between T1 RAS space and surface RAS space
  • dura_file: (str) path to dura surface (for example, the smoothed pial surface). This surface will be used to generate the 3D grid
  • pial_file: (str, optional) path to pial surface (in particular, the lh.pial or rh.pial from freesurfer). You need to specify key morphology in parameters.json. Default: None
  • func_file: (str, optional) path to angiogram or fMRI (in NIfTI format). You need to specify key functional in parameters.json. Default: None
• initial (required by command grid3d, fit)
  • label: (str) label for the reference electrode
  • RAS: (list) initial location for the reference electrode (coordinates in MRI space)
  • rotation: (float) degree of rotation of the grid (in degrees, 0° is roughly pointing up)
• morphology
  • distance: (str, optional) how to compute the distance of the morphology. Values: [ray, minimum, view, cylinder, pdf]. Default: ray
  • maximum_distance: (float, optional) maximum distance between electrode and pial surface. Exact interpretation depends on the type of morphology. Default: 10
  • penalty: (float, optional) exponent when computing the penalty from the distance. Morphology = 1 / distance^penalty. More simply, 1 = activity decreases linearly with distance; 2 = activity decreases with the square of the distance. Default: 1
• functional
  • threshold: (float) value to threshold the func_file and binarize it. If None, func_file won’t be binarized. Default: None
  • metric: (str, optional) method to compute the value at each electrode. sphere is the sum of the voxels around the electrodes, within kernel distance. gaussian is the weighted average of the voxels around an electrode, weighted by a 3d gaussian kernel. With inverse, the weights are based on the inverse of the distance.. Values: [gaussian, sphere, inverse]. Default: inverse
  • kernel: (float, optional) With method sphere, this is the size of the sphere. With method gaussian, this is the size of the sigma of the 3D weighting kernel. With method inverse, this is the exponent (1 -> linear, 2 -> quadratic).. Default: 2
• fit (required by command fit)
  • method: (str) method to use (brute includes simplex as a second step). Values: [brute, simplex]. Default: brute
  • metric: (str, optional) ‘parametric’ correlation (Pearson, default), ‘nonparametric’ correlation (rank) or ‘sum’ (grid position where the sum of the electrode values is highest). Values: [parametric, nonparametric, sum]. Default: parametric
  • morphology_weight: (float, optional) whether morphology is positively (+1) or negatively (-1) correlated to ECoG (or whether morphology contributes positively or negatively to the highest sum). You can also adjust this value to adjust the scale of the morphology values.. Default: 1
  • functional_weight: (float, optional) whether functional is positively (+1) or negatively (-1) correlated to ECoG (or whether functional contributes positively or negatively to the highest sum). You can also adjust this value to adjust the scale of the functional values.. Default: 1
  • functional_contribution: (list, optional) If both present, it’s possible to combine morphology and functional models with varying weights. This parameter indicates which weights will be tested (10 = 10% of functional contribution and 90% of morphology contribution). Default: [0, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100]
  • steps
    • x: (float, optional) Step size in mm for x-direction, for method simplex
    • y: (float, optional) Step size in mm for y-direction, for method simplex
    • rotation: (float, optional) Step size in degrees for rotation, for method simplex
  • ranges
    • x: (list, optional) Range in mm for x-direction, in format [low, step, high], for method brute
    • y: (list, optional) Range in mm for y-direction, in format [low, step, high], for method brute
    • rotation: (list, optional) Range in degrees for rotation, in format [low, step, high], for method brute
• matlab (required by command matlab)
  • input
    • subjectInfo_file: (str) path to subjectInfo.mat (can also be subj_info.json if subjectInfo.mat is not available)
    • gridInfo_file: (str) path to gridInfo.mat
  • comparison
    • angiomap_file: (str, optional) path to _angiomap.mat
    • model_file: (str, optional) path to full models (“ROI”)
    • prediction_file: (str, optional) path to coordinates with the best fit

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