spm_fmri_concatenate.m

function [SPM] = spm_fmri_concatenate(P, scans);
% Adjust an SPM.mat which has concatenated sessions.
% FORMAT spm_post_concatenate(P, scans)
% Session regressors are added and the high-pass filter and non-sphericity
% estimates adjusted as if sessions are separate.
%
% P     - filename of the SPM.mat file to adjust
% scans - [1 x n] vector with the original number of scans in each session
%
% The expected workflow is:
%
% 1. Manually specify a GLM with timeseries and onsets concatenated
% 2. Run spm_post_concatenate on the saved SPM.mat.
% 3. Estimate the SPM.mat in the normal way.
%
% Tips:
%
% - The BOLD-response may overhang from one session to the next. To reduce
%   this, acquire additional volumes at the end of each session and / or
%   add regressors to model the trials at the session borders.
%__________________________________________________________________________
% Copyright (C) 2015-2017 Wellcome Trust Centre for Neuroimaging

% Guillaume Flandin & Peter Zeidman
% $Id: spm_fmri_concatenate.m 7018 2017-02-15 13:36:48Z guillaume $


%-Input parameters
%==========================================================================

%-Get SPM.mat
%--------------------------------------------------------------------------
if ~nargin || isempty(P)
    [P, sts] = spm_select(1,'^SPM\.mat$','select SPM.mat');
    if ~sts, return; end
end
if iscell(P), P = P{1}; end

%-Get number of scans per session
%--------------------------------------------------------------------------
if nargin < 2
    scans = spm_input('scans per session','!+0','r');
end

% Load SPM.mat
%--------------------------------------------------------------------------
SPM = load(P);

% Validate
%--------------------------------------------------------------------------
try
    SPM = SPM.SPM;
catch
    error('Input file is not a valid SPM.mat.');
end

if ~isfield(SPM,'Sess') || numel(SPM.nscan) ~= 1
    error('Input file is not a single session fMRI SPM.mat.');
end

if sum(scans) ~= SPM.nscan
    error('Number of scans does not match.');
end

% Create backup
%--------------------------------------------------------------------------
copyfile(P, fullfile(spm_file(P,'fpath'),'SPM_backup.mat'));


%-Session-specific whitening and filtering
%==========================================================================

SPM.nscan = scans;

% Session-specific grand mean scaling (see spm_fmri_spm_ui.m)
%--------------------------------------------------------------------------

% Session effects (see spm_fMRI_design.m)
%--------------------------------------------------------------------------
if numel(SPM.xX.iB) == 1 && SPM.xX.iB == size(SPM.xX.X,2)
    Xb = [];
    Bn = {};
    for s=1:numel(SPM.nscan)
        Xb      = blkdiag(Xb,ones(SPM.nscan(s),1));
        Bn{s}   = sprintf('Sn(%i) constant',s);
    end
    SPM.xX.X    = [SPM.xX.X(:,1:end-1) Xb];
    SPM.xX.iB   = SPM.xX.iB:(SPM.xX.iB+size(Xb,2)-1);
    SPM.xX.name = {SPM.xX.name{1:end-1} Bn{:}};
end

% High-pass filter (see spm_spm.m)
%--------------------------------------------------------------------------
s = cumsum([0 SPM.nscan]);

for i=1:numel(SPM.nscan)
    K(i) = struct('HParam', SPM.xX.K(1).HParam,...
                  'row',    s(i) + (1:SPM.nscan(i)),...
                  'RT',     SPM.xY.RT);
end
SPM.xX.K = spm_filter(K);

% Temporal non-sphericity (see spm_spm.m)
%--------------------------------------------------------------------------
switch lower(SPM.xVi.form)
    case {'ar(1)','ar(0.2)'}
        SPM.xVi.Vi   = spm_Ce('ar',SPM.nscan,0.2);
        SPM.xVi.form = 'AR(0.2)';
    case 'fast'
        SPM.xVi.Vi   = spm_Ce('fast',SPM.nscan,SPM.xY.RT);
    case {'i.i.d', 'none'}
    otherwise
        warning('Unhandled temporal non-sphericity.');
end

% Set back nscan as if single session
%--------------------------------------------------------------------------
%SPM.nscan = sum(SPM.nscan);


%-Save
%==========================================================================
save(P, 'SPM', spm_get_defaults('mat.format'));
disp('SPM.mat adjusted for sessions: Please estimate to apply changes.');