filter_loop: Loop through reference slices

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

Description

This function will take a filter and loop through all images in a partial brain or just the reference images across the brain in either the registration or segmentation channel. The user can check qualitatively whether the filter needs adjustment after every image check. There is a console menu option for the user to adjust filter parameters if they need. If the filter has been changed by the user, either through the GUI or through the console menu, the function can reloop through the start of the image sequence.

Usage

filter_loop(setup, channel = c("regi", "seg"), filter = NULL, console = TRUE)

Arguments

setup	(required) Setup list from setup_pl().
channel	(optional, default = "regi") Which channel you are checking the filter for.
filter	(optional, default = NULL) User entered custom filter.
console	(optional, default = TRUE) Display console interface to modify filter parameters instead of using the built-in GUI.

Value

Returns filter with adjusted values.

See Also

See also the wholebrain::segment() function in wholebrain.

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