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