How to check the progress of fixelcfestats

1

Hi,
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,
Mahmoud

2

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.

3

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?

Thanks,
Mahmoud

4

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.

It won’t change the number of fixels if you still run the command with the same input fixel directory. It will however influence which of those fixels contain fixel-fixel connectivity, and hence how much RAM is required.

How should I check the files in the output directory? by mrview or mrstats?

Given you’re checking for the presence of extreme values, you’re more likely to catch such using mrstats than by trying to find them manually using mrview.

which file has T-values?

The output fixel directory should contain a fixel data file called tvalue.mif.