SurfClust Question

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Howdy-

*.niml.dset files can be used with clustering. They contain information at nodes, values that can be thresholded, for example. You also need the information of the topology/relatedness of mesh nodes, which are contained in *.gii files or in groups of GII files, the latter of which can be loaded in with *.spec files.

From this Message Board question, here is an example call to SurfClust:

SurfClust                                     \
    -i      ./std.60.lh.smoothwm.gii          \
    -input  ./std.60.lh.thickness.niml.dset 0 \
    -rmm    -1.000000  \
    -thresh_col 0      \
    -athresh 3.580000  \
    -amm2 50.000000    \
    -sort_area         \
    -no_cent

… where the following are input: a dset (./std.60.lh.thickness.niml.dset, which is the dset that is thresholded (here at 3.58) + clusterized (here with NN=1, from ‘-rmm -1’)), which is overlaid on the “underlay” data set (std.60.lh.smoothwm.gii) that contains the mesh information, and the other options are described in the help file. Note how with the -input .. dset, you also specify which subvolume is used for clusterizing (even if there is only a single volume there, so you select the 0-th vol):

     -input inData.dset dcol_index: The input dataset
                                  and the index of the
                                  datacolumn to use
                                  (index 0 for 1st column).
                                  Values of 0 indicate 
                                  inactive nodes.

If your -input .. dset had more than one value per node (like a time series, for example), you could select a different subvolume from it for clusterizing.

–pt

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