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reference:ft_volumelookup [2018/08/23 14:43]
reference:ft_volumelookup [2018/08/23 14:43] (current)
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 +=====  FT_VOLUMELOOKUP =====
 +
 +Note that this reference documentation is identical to the help that is displayed in MATLAB when you type "help ft_volumelookup"​.
 +
 +<​html><​pre>​
 +  <a href=/​reference/​ft_volumelookup><​font color=green>​FT_VOLUMELOOKUP</​font></​a>​ 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 <a href=/​reference/​ft_read_mri><​font color=green>​FT_READ_MRI</​font></​a>​ source is the output of <a href=/​reference/​ft_sourceanalysis><​font color=green>​FT_SOURCEANALYSIS</​font></​a>​
 +    stat   is the output of <a href=/​reference/​ft_sourcestatistics><​font color=green>​FT_SOURCESTATISTICS</​font></​a>​
 + 
 +  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 <a href=/​reference/​ft_read_atlas><​font color=green>​FT_READ_ATLAS</​font></​a>​
 +    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 <a href=/​reference/​ft_read_atlas><​font color=green>​FT_READ_ATLAS</​font></​a>​
 +    cfg.maskparameter ​      = string, field in volume to be looked up, data in field should be logical
 +    cfg.minqueryrange ​      = number, should be odd and &lt;= to maxqueryrange (default = 1)
 +    cfg.maxqueryrange ​      = number, should be odd and &gt;= 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 <a href=/​reference/​ft_read_atlas><​font color=green>​FT_READ_ATLAS</​font></​a>​
 +    cfg.minqueryrange ​      = number, should be odd and &lt;= to maxqueryrange (default = 1)
 +    cfg.maxqueryrange ​      = number, should be odd and &gt;= 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 <a href=/​reference/​ft_read_atlas><​font color=green>​FT_READ_ATLAS</​font></​a>,​ <a href=/​reference/​ft_sourceplot><​font color=green>​FT_SOURCEPLOT</​font></​a>​
 +</​pre></​html>​