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