seg_loop: Loop through and segment images in the segmentation channel

In mjin1812/SMART: SMART (Semi-manual alignment to reference template): a pipeline for whole brain mapping projects

Description

Loop through the z images in the segmentation folder path. For a whole brain, every N images is segmented, where N is equal to setup$seg_step. For a partial brain, all the images in setup$regi_z are segmented. The function will return a list called segs of length 2. Note: if the imaging dataset is large this will be a time intensive process. Processing time will be printed once the function is finished.

Usage

seg_loop(
  setup,
  filter,
  numthresh = 8,
  downsample = 0.25,
  post = NULL,
  pre = NULL,
  get.contour = FALSE,
  channel = 0
)

Arguments

setup	(required) Setup list from setup_pl().
filter	(required) Filter optimized for segmentation of images in the segmentation channel.
numthresh	(optional, default = 8) Original argument from wholebrain::segment().
downsample	(optional, default = 0.25) Original argument from wholebrain::segment().
post	(optional, default = NULL) Original argument from wholebrain::segment().
pre	(optional, default = NULL) Original argument from wholebrain::segment().
get.contour	(optional, default = FALSE) Original argument from wholebrain::segment().
channel	(optional, default = 0) Original argument from wholebrain::segment().

Value

returns segs A list of length 2. Each list element is described below:

1. A vector of the z-image number corresponding to each segmented slice stored in the 2nd element.

2. A list of segmentation information for each segmentated image.

See Also

See also the wholebrain::segment() function.

mjin1812/SMART documentation built on Oct. 30, 2021, 7:25 p.m.