Hi-

Do you want the average time series per ROI? There are different ways to do this, but most will not make a "ROI=0" time series. The label is there, as every voxel has a label, though. I would probably use 3dNetCorr with one or more of the following options:

-ts_out          :switch to output the mean time series of the ROIs that
                      have been used to generate the correlation matrices.
                      Output filenames mirror those of the correlation
                      matrix files, with a '.netts' postfix.

    -ts_label        :additional switch when using '-ts_out'. Using this
                      option will insert the integer ROI label at the start
                      of each line of the *.netts file created. Thus, for
                      a time series of length N, each line will have N+1
                      numbers, where the first is the integer ROI label
                      and the subsequent N are scientific notation values.

    -ts_indiv        :switch to create a directory for each network that
                      contains the average time series for each ROI in
                      individual files (each file has one line).
                      The directories are labelled PREFIX_000_INDIV/,
                      PREFIX_001_INDIV/, etc. (one per network). Within each
                      directory, the files are labelled ROI_001.netts,
                      ROI_002.netts, etc., with the numbers given by the
                      actual ROI integer labels.

You will have a time series for every non-zero ROI where there is data (and see the other options about controlling behavior if the data is masked and some time series are all zero).


Re. the atlas:
Thanks, that is a good point. I had downloaded it separately from the website, and am not sure why that version didn't have labels... But indeed, when I run:

3dinfo -labeltable MNI_caez_ml_18+tlrc. | wc -l

.... I get 119 lines, of which 4 are header/footer ones, so there are 115 labels there. If I check explicitly for a ROI=0 label here with:

3dinfo -labeltable MNI_caez_ml_18+tlrc. | grep "\"0\""

... I get nothing, so there really do appear to be 115 labels. You can see what they are with (and ignore the first line; on a Mac, the "head" command has limited functionality---*sigh*):
3dinfo -labeltable MNI_caez_ml_18+tlrc. | tail -n+4 | tr "\"" " " | sort -n

But indeed, there does appear to be an ROI=116, from looking at the max value in the dset, and it doesn't have a label attached to it. We will discuss this and see why that is... Thanks for bringing this up!

--pt