cmind.pipeline.cmind_crop_robust

Functions

cmind_crop_robust(fname, fname_crop[, ...])

utility to reduce FOV in S/I direction, removing some of the neck

cmind.pipeline.cmind_crop_robust.cmind_crop_robust(fname, fname_crop, age_months=252, z_crop_mm=None, oname_root='T1W', minthresh=0.03, fname2=None, fname2_crop=None, oname2_root='T2W', generate_figures=True, ForceUpdate=False, verbose=False, logger=None)

utility to reduce FOV in S/I direction, removing some of the neck

Parameters:

fname : str

input filename

fname_crop : str

output filename. if a directory name is given instead, a file named `oname_root`+_Structural_Crop.nii.gz will be created in that folder

age_months : float

subject age in months

z_crop_mm : int, optional

size to crop to in mm. If specified overrides the automatic setting via age_months

oname_root : str, optional

output filename prefix

minthresh : float, optional

percentage threshold below which to consider intensities to be noise. This is used when detecting the number of “empty” slices above the head.

fname2 : str, optional

second input file to apply the identical fslroi crop to

fname2_crop : str, optional

output filename for the second input

oname2_root : str, optional

output filename prefix for fname2

generate_figures : bool, optional

if true, generate additional summary images

ForceUpdate : bool,optional

if True, rerun and overwrite any previously existing results

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:

fname_crop : str

filename of the cropped image

Notes

Crops the FOV in S/I direction by an age-dependent amount. This is a rough crop and is not intended to remove all of the neck, etc.

T1-weighted head prior to crop

T1-weighted head after crop