spm_spm: SPM: [Re]ML Estimation of a General Linear Model

Description Usage Arguments Value

Description

Required fields of SPM:

xY.VY - nScan x 1 struct array of image handles (see spm_vol) Images must have the same orientation, voxel size and data type - Any scaling should have already been applied via the image handle scalefactors.

xX - Structure containing design matrix information - Required fields are: xX.X - Design matrix (raw, not temporally smoothed) xX.name - cellstr of parameter names corresponding to columns of design matrix - Optional fields are: xX.K - cell of session-specific structures (see spm_filter) - Design & data are pre-multiplied by K (K*Y = K*X*beta + K*e) - Note that K should not smooth across block boundaries - defaults to speye(size(xX.X,1)) xX.W - Optional whitening/weighting matrix used to give weighted least squares estimates (WLS). If not specified spm_spm will set this to whiten the data and render the OLS estimates maximum likelihood i.e. W*W' = inv(xVi.V).

xVi - Structure describing intrinsic temporal non-sphericity - Required fields are: xVi.Vi - array of non-sphericity components - defaults to speye(size(xX.X,1)) - i.i.d. - specifying a cell array of constraints (Qi) These constraints invoke spm_reml to estimate hyperparameters assuming V is constant over voxels. that provide a high precise estimate of xX.V - Optional fields are: xX.V - Optional non-sphericity matrix. Cov(e) = sigma^2*V If not specified spm_spm will compute this using a 1st pass to identify significant voxels over which to estimate V. A 2nd pass is then used to re-estimate the parameters with WLS and save the ML estimates (unless xX.W is already specified).

xM - Structure containing masking information, or a simple column vector of thresholds corresponding to the images in VY [default: -Inf] - If a structure, the required fields are: xM.TH - nVar x nScan matrix of analysis thresholds, one per image xM.I - Implicit masking (0=>none, 1 => implicit zero/NaN mask) xM.VM - struct array of explicit mask image handles - (empty if no explicit masks) - Explicit mask images are >0 for valid voxels to assess. - Mask images can have any orientation, voxel size or data type. They are interpolated using nearest neighbour interpolation to the voxel locations of the data Y. - Note that voxels with constant data (i.e. the same value across scans) are also automatically masked out.

swd - Directory where the output files will be saved [default: pwd] If exists, it becomes the current working directory.

In addition, global SPM "defaults" variable is used (see spm_defaults):

stats.<modality>.UFp - critical F-threshold for selecting voxels over which the non-sphericity is estimated (if required) [default: 0.001]

stats.maxres - maximum number of residual images for smoothness estimation

stats.maxmem - maximum amount of data processed at a time (in bytes)

modality - SPM modality 'PET','FMRI','EEG'

Usage

1
FORMAT [SPM] = spm_spm(SPM)

Arguments

SPM

Value

SPM


jpellman/spmR documentation built on May 19, 2019, 10:44 p.m.