Threshold

Interface of AimsThreshold command

Description

Not binary mode : output_image result preserves the levels of gray

Binary mode : output_image is binary (only black and white voxels)

Threshold : selection of one or two tresholds (case of between and outside)

Threshold + Not binary mode : selected voxels are in grey level and the others are black

Threshold + Binary mode : selected voxels are white and the others are black

Selection of threshold : a image is composed with grey levels from 0 to 4095 (for example image). The grey level '0' is in fact black color and the '4095' is white color, all others grey levels are between 1 and 4094. To know the minimun and the maximun of grey level, you can put your image in a browser in Anatomist and read tex_min (black) and tex_max (white) attributes. To handle grey levels of your image, use ROI module of Anatomist (option Connectivity Threshold).

Test image, tex_min = 0, tex_max = 4095

Mode	Description	Mode_no_binary : fasle	Mode_binary : true
less_than	to select all the voxels for which value of levels of gray is smaller than the threshold	Threshold1 = 350	Threshold1 = 350
less_or_equal	to select all the voxels for which value of levels of gray is smaller or equal to the threshold1	Threshold1 = 350	Threshold1 = 350
great_than	to select all the voxels for which value of levels of gray is larger than the threshold1	Threshold1 = 350	Threshold1 = 350
great_or_equal	to select all the voxels for which value of levels of gray is larger or equal to the threshold1	Threshold1 = 350	Threshold1 = 350
equal	to select all the voxels for which value of levels of gray is equal to the threshold	Threshold1 = 350	Threshold1 = 350
different	to select all the voxels for which value of levels of gray is different to the threshold	Threshold1 = 1800	Threshold1 = 1800
between	to select all the voxels for which value of levels of gray contained between 1 and 2	Threshold1 = 391 Threshold2 = 1078	Threshold1 = 391 Threshold2 = 1078
outside	select all voxels with a grey level outside threshold1 and threshold2	Threshold1 = 391 Threshold2 = 1078	Threshold1 = 391 Threshold2 = 1078

Parameters

image_input: 4D Volume ( input )

Mandatory
input data

image_output: 4D Volume ( output )

Mandatory
output data

mode: Choice ( input )

Mandatory : mode of threshold
lt : lower than
le : lower or equal to
gt : greater than
eq : equal to
di : differ
be : between
ou : outside

threshold1: Float ( input )

Mandatory
grey level 1

threshold2: Float ( optional, input )

Optional except for between and outside modes:
grey level 2

binary: Boolean ( optional, input )

Optional
return a short binary data

background_value: Float ( input )

foreground_value: Integer ( input )

Technical information

Toolbox : Tools

User level : 1

Identifier : threshold

File name : brainvisa/toolboxes/tools/processes/threshold.py

Supported file formats :

image_input :

gz compressed NIFTI-1 image, Aperio svs, BMP image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, FreesurferMGH, FreesurferMGZ, GIF image, GIS image, Hamamatsu ndpi, Hamamatsu vms, Hamamatsu vmu, JPEG image, Leica scn, MINC image, NIFTI-1 image, PBM image, PGM image, PNG image, PPM image, SPM image, Sakura svslide, TIFF image, TIFF image, TIFF(.tif) image, TIFF(.tif) image, VIDA image, Ventana bif, XBM image, XPM image, Zeiss czi, gz compressed MINC image, gz compressed NIFTI-1 image

image_output :

gz compressed NIFTI-1 image, BMP image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIF image, GIS image, JPEG image, MINC image, NIFTI-1 image, PBM image, PGM image, PNG image, PPM image, SPM image, TIFF image, TIFF(.tif) image, VIDA image, XBM image, XPM image, gz compressed MINC image, gz compressed NIFTI-1 image