README.md

Brain Plot

Creates a plot of an fMRI dataset à la J.D. Power's "The Plot", https://doi.org/10.1016/j.neuroimage.2016.08.009

Requirements

• SPM version >= 8
• Matlab version >= 7.6

Use

To use, instantiate an object of the class by passing in a scalar opts structure with plot parameters, and call the public method make. An empty opts structure can be obtained by calling the static method defaults, and modifying the structure suitably. E.g.,

Assume that in the current working directory, we have three masks: gray_mask.nii, white_mask.nii, and csf_mask.nii; a realigment parameters file rp.txt; and our SPM.mat.

    % Set up plot parameters
    load SPM.mat
    rp = load('rp.txt');
    opts = BrainPlot.defaults(); % Get the defaults structure.
    opts.brain.vols = spm_vol(SPM.xY.VY);
    opts.mask.vols = spm_vol(spm_select('FPList', pwd, '^.*_mask.nii$'));
    opts.mask.labels = cellstr(spm_select('List', pwd, '^.*_mask.nii$'));
    opts.mask.labels = cellfun(@(s)strrep(s, '_', ' '), opts.mask.labels, ...
                            'UniformOutput',false);
    opts.filter.filter = 1; % We will apply the high pass filter
    opts.whiten.whiten = 1; % We will apply the whitening matrix
    opts.adjust.adjust = 1; % We will adjust for confounds (like motion parameters)
    opts.adjust.contrast = 5;  % We will use an F-contrast indexed 5 to adjust.
    opts.spmpath = '/path/to/SPM.mat';
    opts.extra(1).data = rp(:,1:3);
    opts.extra(1).ylabel = 'translation rp';
    opts.extra(2).data = rp(:,4:6);
    opts.extra(2).ylabel = 'rotation rp';

    % Instantiate the object, make the plot, and save.
    bp = BrainPlot(opts);
    bp.make(); % May take a while.
    bp.save(fullfile(pwd, '1234.jpg'));

For more information about the opts structure, call: help BrainPlot.defaults, or look at the code.