:orphan: .. _ahelp_@T1scale: ******** @T1scale ******** .. contents:: :local: | .. code-block:: none 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