AFNI program: @T1scale
Output of -help
Usage: @T1scale <-T1 T1vol> <-PD PDvol>
Fix bias field shading in T1 by scaling it with PD image.
You can also get a decent result even without the PD volume.
-T1 T1vol: The T1 volume
-PD PDvol: The PD volume (aligned to T1)
-odir ODIR: Directory where output gets dumped.
Default is T1scale/
ODIR will contain multiple volumes with the one
of most interest being T1.uni+orig
Script will reuse existing volumes
-align: Align PD volume to T1. Script assumes volumes are in
close alignment. With this option, output PD+orig volume
will be in alignment with T1+orig.
Without this option, PDvol is assumed in alignment with T1vol
-mask MVOL: Create mask for the output
If not specified, the script will generate one with
3dAutomask on fattened PDvol.
-head_mask: Create mask using 3dSkullStrip's -head option.
-unmasked_uni: Do not apply masking to uniformized volume (default)
You can mask the output after you decide which mask
is best. Here is an example with smask:
3dcalc -a T1.uni+orig. -b smask+orig. \
-expr 'step(b)*a' -prefix T1.uni.m
-masked_uni: Apply masking to uniformized volume
-echo: Set echo
-help: this message
Global Help Options:
-h_web: Open webpage with help for this program
-hweb: Same as -h_web
-h_view: Open -help output in a GUI editor
-hview: Same as -hview
-all_opts: List all of the options for this script
-h_find WORD: Search for lines containing WORD in -help
output. Seach is approximate.
This page auto-generated on
Wed Jul 28 19:40:54 EDT 2021