FT_VOLUMELOOKUP
Note that this reference documentation is identical to the help that is displayed in MATLAB when you type “help ft_volumelookup”.
FT_VOLUMELOOKUP can be used in to combine an anatomical or functional atlas with the source reconstruction results. You can use it for forward and reverse lookup. Given the region of interest (ROI) as anatomical or functional label, it looks up the locations and creates a mask (as a binary volume) based on the label. Given the ROI as point in the brain, it creates a sphere or box around that point. In these two case the function is to be used as: mask = ft_volumelookup(cfg, volume) Given a binary volume that indicates a ROI or a point of interest (POI), it looks up the corresponding anatomical or functional labels from the atlas. In this case the function is to be used as: labels = ft_volumelookup(cfg, volume) In both cases the input volume can be: mri is the output of FT_READ_MRI source is the output of FT_SOURCEANALYSIS stat is the output of FT_SOURCESTATISTICS The configuration options for a mask according to an atlas: cfg.inputcoord = 'mni' or 'tal', coordinate system of the mri/source/stat cfg.atlas = string, filename of atlas to use, see FT_READ_ATLAS cfg.roi = string or cell-array of strings, ROI from anatomical atlas The configuration options for a spherical/box mask around a POI: cfg.roi = Nx3 vector, coordinates of the POI cfg.sphere = radius of each sphere in cm/mm dep on unit of input cfg.box = Nx3 vector, size of each box in cm/mm dep on unit of input cfg.round2nearestvoxel = 'yes' or 'no' (default = 'no'), voxel closest to point of interest is calculated and box/sphere is centered around coordinates of that voxel The configuration options for labels from a mask: cfg.inputcoord = 'mni' or 'tal', coordinate system of the mri/source/stat cfg.atlas = string, filename of atlas to use, see FT_READ_ATLAS cfg.maskparameter = string, field in volume to be looked up, data in field should be logical cfg.minqueryrange = number, should be odd and <= to maxqueryrange (default = 1) cfg.maxqueryrange = number, should be odd and >= to minqueryrange (default = 1) The configuration options for labels around POI: cfg.output = 'single' always outputs one label; if several POI are provided, they are considered together as describing a ROI (default) 'multiple' outputs one label per POI (e.g., choose to get labels for different electrodes) cfg.roi = Nx3 vector, coordinates of the POI cfg.inputcoord = 'mni' or 'tal', coordinate system of the mri/source/stat cfg.atlas = string, filename of atlas to use, see FT_READ_ATLAS cfg.minqueryrange = number, should be odd and <= to maxqueryrange (default = 1) cfg.maxqueryrange = number, should be odd and >= to minqueryrange (default = 1) cfg.querymethod = 'sphere' searches voxels around the ROI in a sphere (default) = 'cube' searches voxels around the ROI in a cube cfg.round2nearestvoxel = 'yes' or 'no', voxel closest to POI is calculated (default = 'yes') The label output has a field "names", a field "count" and a field "usedqueryrange". To get a list of areas of the given mask you can do for instance: [tmp ind] = sort(labels.count,1,'descend'); sel = find(tmp); for j = 1:length(sel) found_areas{j,1} = [num2str(labels.count(ind(j))) ': ' labels.name{ind(j)}]; end In the "found_areas" variable you can then see how many times which labels are found. Note that in the AFNI brick one location can have 2 labels. Dependent on the input coordinates and the coordinates of the atlas, the input MRI is transformed betweem MNI and Talairach-Tournoux coordinates See http://www.mrc-cbu.cam.ac.uk/Imaging/Common/mnispace.shtml for more details. See http://www.fieldtriptoolbox.org/template/atlas for a list of templates and atlasses that are included in the FieldTrip release. See also FT_READ_ATLAS, FT_SOURCEPLOT