Hi, Steph-
OK, that sounds like you are doing the correct things, and the output does sound a bit odd.
What does this mean: "Freesurfer annotation file with 300 parcels"? The map of target ROIs among which one wants to search for pairwise connections should be a file of integer values, and each ROI is defined as the set of voxels with a given integer. String labels can be attached to each ROI through a labeltable. Output things can have the string label used (e.g., if using the "-dump_rois .." option, which I often find useful), as well as in the output file of matrices (*.grid file).
And yes, the "-netrois ..." argument is used to provide the map of target ROIs.
In the *.grid file, there should be one integer label per ROI; also, there can be one string label per ROI (ROIs without other string labels just get a zero-padded version of their integer value as a string label). If there are more ROIs than you are expecting (and how are you counting these?), is it possible that the parc300.nii.gz file does *not* contain an integer at every voxel? Sometimes alignment/mapping without the nearest neighbor (NN) interpolation, for example, can result in that.
If you have Python and matplotlib on your computer, what does this produce?:
fat_mat_sel.py --matr_in '3dTrackID_prob_000.grid' --Pars 'FA' \
--A_plotmin=0.2 --B_plotmax=1 --dpi_file=200 -x 30
(It should be a large-ish matrix plot of FA values.)
I will also send you a PM with instructions on how you can upload data files and I can take a look at the *.grid output and the parc300.nii.gz file.
Also, part of your message appears to have been truncated-- if you have any other questions, please feel free to ask them.
--pt
