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 source reconstruction. You can use it for forward and reverse
  lookup.
 
  Given the anatomical or functional label, it looks up the locations and
  creates a mask (as a binary volume) based on the label, or creates a
  sphere or box around a point of interest. In this case the function is to
  be used as:
    mask = ft_volumelookup(cfg, volume)
 
  Given a binary volume that indicates a region of interest, it looks up
  the corresponding anatomical or functional labels from a given atlas. In
  this case the function is to be used as follows:
     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, either the AFNI
                      brik file that is available from http://afni.nimh.nih.gov/afni/doc/misc/ttatlas_tlrc,
                      or the WFU atlasses available from  http://fmri.wfubmc.edu. see FT_READ_ATLAS
    cfg.roi        = string or cell of strings, region(s) of interest from anatomical atlas
 
  The configuration options for a spherical/box mask around a point of interest:
    cfg.roi                = Nx3 vector, coordinates of the points of interest
    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, either the AFNI
                         brik file that is available from http://afni.nimh.nih.gov/afni/doc/misc/afni_ttatlas/,
                         or the WFU atlasses available from http://fmri.wfubmc.edu. see FT_READ_ATLAS
    cfg.maskparameter = string, field in volume to be lookedup, data in field should be logical
    cfg.maxqueryrange = number, should be 1, 3, 5 (default = 1)
 
  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 found_areas you can then see how many times which labels are found
  NB 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 also FT_READ_ATLAS, FT_SOURCEPLOT

reference/ft_volumelookup.txt · Last modified: 2016/08/17 23:02 (external edit)

You are here: startreferenceft_volumelookup
CC Attribution-Share Alike 3.0 Unported
www.chimeric.de Valid CSS Driven by DokuWiki do yourself a favour and use a real browser - get firefox!! Recent changes RSS feed Valid XHTML 1.0
This DokuWiki features an Anymorphic Webdesign theme, customised by Eelke Spaak and Stephen Whitmarsh.
Mobile Analytics Website Security Test