Hi, I wanted to test out the newest version of fixelcfestats, which seemed like it would be sleeker given that fixel-fixel connectivity doesn’t need to be computed each time the command is executed. When I run my model in the older version, it takes about 1hr/contrast (to calculate fixel-fixel connectivity and run the permutations for that contrast). I reran the same analysis in the new version of MRtrix3, allocating the same 40G of memory that I always do for fixelcfestats (with all the contrasts represented in a single matrix), and the process has been crawling through the first set of permutation calculations for over four days. The process isn’t “hung”, because there has been incremental creeping forward of the progress bar. Any ideas for why this might be? Full info below…

##command

fixelcfestats -force -nshuffles 1000 $DIR/fd_smooth/ $DIR/scripts_fixel/fixel_1208_fd.txt $DIR/scripts_fixel/design_1208_ones_sex_age_raceAA_raceOT_qc_wrat.txt $DIR/scripts_fixel/contrast_matrix_0000000b.txt $DIR/population_template/matrix $DIR/fixelcfe_output_smooth/fixelcfestats_1208_ones_sex_age_raceAA_raceOT_qc_wrat_fdB_2 -nthreads 2

##contrast matrix

cat contrast_matrix_0000000b.txt

0 0 0 0 0 0 1

0 0 0 0 0 0 -1

0 0 0 0 0 1 0

0 0 0 0 0 -1 0

0 0 0 0 1 0 0

0 0 0 0 -1 0 0

0 0 0 1 0 0 0

0 0 0 -1 0 0 0

0 0 1 0 0 0 0

0 0 -1 0 0 0 0

0 1 0 0 0 0 0

0 -1 0 0 0 0 0

##output after running for over four days:

cat fixelcfestats_1208_ones_sex_age_raceAA_raceOT_qc_wrat_fdB.txt

fixelcfestats: [WARNING] existing output files will be overwritten

fixelcfestats: Number of fixels in template: 173239

fixelcfestats: Importing data from files listed in “fixel_1208_fd.txt” as found relative to directory “/gpfs/ysm/scratch60/pittenger/rgg27/PNC/fixel//fd_smooth/”… …done

fixelcfestats: Number of inputs: 1208

fixelcfestats: Number of factors: 7

fixelcfestats: Design matrix condition number: 13.7053

fixelcfestats: Number of hypotheses: 12

fixelcfestats: [WARNING] A total of 5180 fixels do not possess any streamlines-based connectivity; these will not be enhanced by CFE, and hence cannot be tested for statistical significance

fixelcfestats: Loading fixel data (no smoothing)… [==================================================]

fixelcfestats: Calculating basic properties of default permutation… [========================================]

fixelcfestats: Outputting beta coefficients, effect size and standard deviation… [=================================================]

fixelcfestats: Running GLM and enhancement algorithm for default permutation… [======================================]

fixelcfestats: Running permutations… [========================================