no data in matrix file mean_FA_per_streamline.csv

I was trying to comput the mean FA values of two brain areas with “dwi2connectome” and “tcksample” and there are some errors after I run the script. I will appreciate that you tell me which steps are wrong or missing.

The source code is:

  • dwi2tensor dwi.mif tensor.mif -mask mask.mif
  • tensor2metric -fa diff_fa.mif.gz tensor.mif
  • tcksample whole_brain.tck diff_fa.mif mean_FA_per_streamline.csv -stat_tck mean
  • tck2connectome whole_brain.tck aparcaseg_2_diff_fsl.mif mean_FA_connectome.csv -scale_file mean_FA_per_streamline.csv -stat_edge mean

There is an error says “no data in matrix file mean_FA_per_streamline.csv” after running the last command.


Have you looked at the contents of your mean_FA_per_streamline.csv file? It should be just text, with a long list of numbers.

If it’s empty, you’ll need to check what’s in your whole_brain.tck file using tckinfo. What does it report in the count field?