How to check the progress of fixelcfestats

I ran fixelcfestats fd files.txt design_matrix.txt contrast_matrix.txt tracks_2_million_sift.tck stats_fd and here is the output on screen:

fixelcfestats: number of fixels: 767739
fixelcfestats: [100%] preloading data for "fd/directions.mif"
fixelcfestats: [100%] loading template fixel directions and positions
fixelcfestats: [done] validating input files
fixelcfestats: [100%] pre-computing fixel-fixel connectivity
fixelcfestats: [100%] normalising and thresholding fixel-fixel connectivity matrix
fixelcfestats: [100%] loading input images and smoothing
fixelcfestats: [done] outputting beta coefficients, effect size and standard deviation

It has been a few hours that there is no progress. How can I know whether it is still running or it faced a problem?

Thank you,

number of fixels: 767739

With this number of fixels, there’s a good chance that your system has run out of RAM and is now swapping, which will slow the command down to a crawl.

How can I know whether it is still running or it faced a problem?

If the above is not the case, take a peek at those fixel data files that have been written to the output directory during the course of the “outputting beta coefficients, effect size and standard deviation” section; in particular the T-value. Sometimes if the design matrix is incorrectly constructed, there can be t-values that are enormous in magnitude, and this makes CFE effectively stall as it attempts to integrate from 0 to some enormous number in 0.1 increments.

Hi Rob,

1- How can I reduce the number of fixels, here? I used tckedit with mask option to create a lighter version of my tracks_2_million_sift.tck but that didn’t change the number of fixels.

2- How should I check the files in the output directory? by mrview or mrstats? which file has T-values?