cmind.pipeline.cmind_calculate_slice_coverage

Functions

cmind_calculate_slice_coverage(inputvol[, ...])

Make overlays of the acquired volume onto the MNI standard space brain

cmind.pipeline.cmind_calculate_slice_coverage.cmind_calculate_slice_coverage(inputvol, standard_maskvol=None, bg_thresh=0.05, fill_holes=False, output_img=None, subjID=None, verbose=False, logger=None)

Make overlays of the acquired volume onto the MNI standard space brain

Parameters:

inputvol : list

list of input volumes to compute slice coverage for

standard_maskvol : str

MNI brain mask image (e.g. MNI152_T1_2mm_brain_mask.nii.gz)

bg_thresh : float

percentage of 95th percentile intensity to mask out as background

fill_holes : bool, optional

fill holes in binary mask after mask=inputvol>(bg_thresh * p95)

output_img : list, optional

list of images to generate. If empty, name will be autogenerated based on inputvol

subjID : str, optional

subject ID to overlay onto the images generated

verbose : bool, optional

print additional output (to terminal and log)

logger : logging.Logger or str, optional

logging.Logger object (or string of a filename to log to)

Returns:

all_frac : array

percent slice coverage for each slice in the MNI brain

missing_slices : list

list of slices that have 25 percent or less coverage

Nmissing_top : int

number of slices missing from the top of the brain