``solid-blob extract'' -- extract bright solid blobs

purpose:

This is the same as ``LV_extract'' except this function has more parameters. In particular, more parameters exist for autothresholding.

The papillary-muscle probe can be used for filling sagittal-plane gaps that extend over up to 7 slices (the probe does a 3x3x7 morphological closing).

Like ``LV extract'', this is an extremely slow function. Use it in the background mode.

input:

An 8-bit volume.

output:

An 8-bit volume. Also, a file called ``invol.size'', which gives the sizes in voxels of the extracted regions; ``invol'' is the name of the input volume. If no input volume name is specified, a file called ``sizeXXXXXX'' is made instead, where XXXXXX is a computer-generated code like g56038.

parameters:

Default parameters menu is

smallest isthmus diameter = 7
use papillary muscle probe = yes
No. of objects to save = 1
clean up areas straddling zeros = yes
use maxh filter = yes
thresholding scheme = auto threshold
*****Auto-thresholding Parameters*****
mode = restrict rise
top-level parameters:
lowest tolerable threshold = 120
cue-slice number = 1
# of slices per group = 2
max intergroup threshold change = 30
max allowed threshold rise(RR mode) = 5
use area-of-interest (mbc) analysis = no
area-of-interest expansion factor = 100
histogram-analysis parameters:
min histogram peak sep (graylevels) = 30
min histogram-peak area(% of total) = 2.00
absolute min peak sep = 16
****Manual-thresholding Parameters****
FIRST threshold:
threshold = 0
beginning slice = 0
SECOND threshold:
threshold = 0
beginning slice = 0
input from vol # = 0
copy output to vol # = 0

comments:

 

1. See comments under ``LV_extract''.