Apologies for the silly question . I am conducting ReHo analysis using 3dReHo. When I use it with the option -in_rois I supply a resampled version of the TTatlas . This dataset has 241 labels as I know from a simple grep on the output of 3dinfo -atlas_points .
But when I process my reho dataset the .vals output file has 237 items.
Another potential issuse I noted is that if I change the default radius size the values in the .vals file do not change at all.
Maybe I am doing something wrong?
thanks a lot!
By default, 3dReHo will calculate “ReHo” (= Kendall’s concordance coefficient) for each voxel in the brain, returning a whole brain map. The ReHo value is over a simple neighborhood of voxels-- you can specify the size of that neighborhood in different ways (“-neigh_* VALUE”, “-nneigh VALUE”, “-neigh_RAD VALUE”, “-box_RAD VALUE”, etc.).
If you want to calculate ReHo over voxels that are not in a “simple” neighborhood, then you can upload maps of regions using the “-in_rois MAP_FILE”. Within each ROI there (where an ROI is defined as a set of voxels in the MAP_FILE having the same integer value), ReHo gets calculated and dumped out in a text file, the *.vals file, because it isn’t a whole brain measure-- it is a per-ROI measure that has been calculated. The radius options and things just refer to the simple neighborhoods above, and have no bearing on the ROI-mapped values-- the neighbood is each ROI.
As to why only 237 out of 241 values were being returned, is it possible that the map of ROIs does not fit perfectly on the time series map, and that there are “empty” ROIs? That would be worth checking in the viewer. I am not certain about this point, however.
Thank you!I will try again with a simpler group of labelmaps as input.
I added the in_ROI options in the 3dReHo program, however i can’t get the .val file. Is there any specific requirement for the input of in_ROI, or the limit number of ROIs.
Thanks a lot!
Can you please post: the output of “afni -ver”; your exact 3dReHo command; and the results that get shown in the terminal when running 3dReHo?