7.1.213. 3dpcΒΆ

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Principal Component Analysis of 3D Datasets Usage: 3dpc [options] dataset dataset ...

Each input dataset may have a sub-brick selector list. Otherwise, all sub-bricks from a dataset will be used.

OPTIONS:

-dmean = remove the mean from each input brick (across space)
-vmean = remove the mean from each input voxel (across bricks)
[N.B.: -dmean and -vmean are mutually exclusive] [default: don’t remove either mean]
-vnorm = L2 normalize each input voxel time series
[occurs after the de-mean operations above,] [and before the brick normalization below. ]
-normalize = L2 normalize each input brick (after mean subtraction)
[default: don’t normalize]
-nscale = Scale the covariance matrix by the number of samples
This is not done by default for backward compatibility. You probably want this option on.
-pcsave sss = ‘sss’ is the number of components to save in the output;
it can’t be more than the number of input bricks [default = none of them]
  • To get all components, set ‘sss’ to a very large number (more than the time series length), like 99999 You can also use the key word ALL, as in -pcsave ALL to save all the components.
-reduce r pp = Compute a ‘dimensionally reduced’ dataset with the top
‘r’ eigenvalues and write to disk in dataset ‘pp’ [default = don’t compute this at all]
  • If ‘-vmean’ is given, then each voxel’s mean will be added back into the reduced time series. If you don’t want this behaviour, you could remove the mean with 3dDetrend before running 3dpc.
  • On the other hand, the effects of ‘-vnorm’ and ‘-dmean’ and ‘-normalize’ are not reversed in this output (at least at present – send some cookies and we’ll talk).
-prefix pname = Name for output dataset (will be a bucket type);
  • Also, the eigen-timeseries will be in ‘pname’_vec.1D (all of them) and in ‘pnameNN.1D’ for eigenvalue #NN individually (NN=00 .. ‘sss’-1, corresponding to the brick index in the output dataset)
  • The eigenvalues will be printed to file ‘pname’_eig.1D All eigenvalues are printed, regardless of ‘-pcsave’. [default value of pname = ‘pc’]
-1ddum ddd = Add ‘ddd’ dummy lines to the top of each *.1D file.
These lines will have the value 999999, and can be used to align the files appropriately. [default value of ddd = 0]
-verbose = Print progress reports during the computations
-quiet = Don’t print progress reports [the default]
-eigonly = Only compute eigenvalues, then
write them to ‘pname’_eig.1D, and stop.
-float = Save eigen-bricks as floats
[default = shorts, scaled so that |max|=10000]
-mask mset = Use the 0 sub-brick of dataset ‘mset’ as a mask
to indicate which voxels to analyze (a sub-brick selector is allowed) [default = use all voxels]

Example using 1D data a input, with each column being the equivalent of a sub-brick:

3dpc -prefix mmm -dmean -nscale -pcsave ALL datafile.1D

++ Compile date = Dec 16 2015

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