7.1.151. 3dTcorr1DΒΆ

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Usage: 3dTcorr1D [options] xset y1D Computes the correlation coefficient between each voxel time series in the input 3D+time dataset ‘xset’ and each column in the 1D time series file ‘y1D’, and stores the output values in a new dataset.

OPTIONS:

-pearson = Correlation is the normal Pearson (product moment)
correlation coefficient [this is the default method].
-spearman = Correlation is the Spearman (rank) correlation
coefficient.
-quadrant = Correlation is the quadrant correlation coefficient.
-ktaub = Correlation is Kendall’s tau_b coefficient.
++ For ‘continuous’ or finely-discretized data, tau_b and
rank correlation are nearly equivalent (but not equal).
-prefix p = Save output into dataset with prefix ‘p’
[default prefix is ‘Tcorr1D’].
-mask mmm = Only process voxels from ‘xset’ that are nonzero
in the 3D mask dataset ‘mmm’.

++ Other voxels in the output will be set to zero.

-float = Save results in float format [the default format].
-short = Save results in scaled short format [to save disk space].

NOTES: * The output dataset is functional bucket type, with one sub-brick

per column of the input y1D file.
– RWCox - Apr 2010
  • Jun 2010: Multiple y1D columns; OpenMP; -short; -mask.
  • This binary version of 3dTcorr1D 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 with ‘cluster’ setups).

  • For implementation and compilation details, please see

    http://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 (such as the NIH Biowulf), it seems to be

    necessary to set 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 ...... 16.

  • The maximum number of CPUs that will be used is now set to .... 7.

++ Compile date = Dec 16 2015

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