COVAR

covar − Compute covariance matrix for a set of volumes

covar [-i level] [-l scalelist] [-m maskfile] [-s meanvol] [-o outputmatrix] [-d] [-p type] file1 file2 ... fileN

Computes N x N empirical covariance matrix between the specified volumes. The matrix is not normalized, i.e. if the files 1..N make up the columns of a data matrix X then the output is (X-<x>)’*(X-<x>) where <x> is the mean across columns of X.

The program is designed to handle large volumes so volumes are read in multiple times. There has to be memory to store 3 volumes, one in internal rep. (for the mean volume of the <x>’s) and two in input raw format/ I.e. if the volumes are byte format, and the mean is stored as 16 bit, the total memory requirement is 2 byte volumes plus one 16 bit volume, i.e. four times one input volume. The internal representation for the mean is chosen automatically, but you can use the -p option to manually specify the internal representation for the mean. Note that <x> is stored as the sum of file1..N i.e. it is integer when the input format is too (and no scaling is applied).

-d

compute only diagonal entries of covariance matrix.

-x max

use no more than ’max’ megabytes of memory.

-p type

specifies the datatype that should be used for internal computation T_BYTE=1, T_USHORT=2, T_SSHORT=3 , T_INT32=4, T_FLOAT=5, T_DOUBLE=6

-m maskfile

The input ’maskfile’ tells covar which voxels to use. This saves memory because the mean vectors are only stored for non-zero mask voxels.

-s meanvol

specifies where to save the computed mean image. Note that for integer datatypes, the output is the sum rather than the mean.

-l scalelist

is an ASCII string containing 1 float per volume (sep by spaces). Each volume in the list is multiplied with this scaling factor before the mean and covariance is computed.

-i level

is the report level, either ’silent’, ’info’ or ’std’.

All volumes have to have same size. Input file format can be VAPET, XPRIME, ANALYZE. All volio input data types are accepted, i.e. byte, ushort, sshort, float, double.

Ulrik Kjems <uk@imm.dtu.dk>

gauss_vol(1), histo_vols(1), subsample(1), file2vapet(1), file2ana(1), file2xprime(1), headerinfo(1), resize_vol(1), convert_vol(1), covar(1), flip(1), region(1), compute_warp(1), warp_reslice(1), warp_reconcile(1),