Usage: 3dMSE [options] dset
Computes voxelwise multi-scale entropy.
Options:
-polort m = Remove polynomial trend of order 'm', for m=-1..3.
[default is m=1; removal is by least squares].
Using m=-1 means no detrending; this is only useful
for data/information that has been pre-processed.
-autoclip = Clip off low-intensity regions in the dataset,
-automask = so that the correlation is only computed between
high-intensity (presumably brain) voxels. The
mask is determined the same way that 3dAutomask works.
-mask mmm = Mask to define 'in-brain' voxels. Reducing the number
the number of voxels included in the calculation will
significantly speedup the calculation. Consider using
a mask to constrain the calculations to the grey matter
rather than the whole brain. This is also preferable
to using -autoclip or -automask.
-prefix p = Save output into dataset with prefix 'p', this file will
contain bricks for both 'weighted' or 'degree' centrality
[default prefix is 'MSE'].
-scales N = The number of scales to be used in the calculation.
[default is 5].
-entwin w = The window size used in the calculation.
[default is 2].
-rthresh r = The radius threshold for determining if values are the
same in the SampleEn calculation, in fractions of the
standard deviation.
[default is .5].
Notes:
* The output dataset is a bucket type of floats.
-- RWCox - 31 Jan 2002 and 16 Jul 2010
-- Cameron Craddock - 26 Sept 2015
=========================================================================
* This binary version of 3dMSE is compiled using OpenMP, a semi-
automatic parallelizer software toolkit, which splits the work across
multiple CPUs/cores on the same shared memory computer.
* OpenMP is NOT like MPI -- it does not work with CPUs connected only
by a network (e.g., OpenMP doesn't work across cluster nodes).
* For some implementation and compilation details, please see
https://afni.nimh.nih.gov/pub/dist/doc/misc/OpenMP.html
* The number of CPU threads used will default to the maximum number on
your system. You can control this value by setting environment variable
OMP_NUM_THREADS to some smaller value (including 1).
* Un-setting OMP_NUM_THREADS resets OpenMP back to its default state of
using all CPUs available.
++ However, on some systems, it seems to be necessary to set variable
OMP_NUM_THREADS explicitly, or you only get one CPU.
++ On other systems with many CPUS, you probably want to limit the CPU
count, since using more than (say) 16 threads is probably useless.
* You must set OMP_NUM_THREADS in the shell BEFORE running the program,
since OpenMP queries this variable BEFORE the program actually starts.
++ You can't usefully set this variable in your ~/.afnirc file or on the
command line with the '-D' option.
* How many threads are useful? That varies with the program, and how well
it was coded. You'll have to experiment on your own systems!
* The number of CPUs on this particular computer system is ...... 1.
* The maximum number of CPUs that will be used is now set to .... 1.
=========================================================================
++ Compile date = Oct 31 2024 {AFNI_24.3.06:linux_ubuntu_24_64}
