Hi @rsmith (@orencivier),
I am attempting to run the connectomestats command to perform TFNBS for a one-sided t-test. The dataset consists of 103 participants and an 84 x 84 connectivity matrix. I am using 500 permutations, 2 CPUs per task, and allocating 12G of memory per CPU. However, the process has been running for 16 hours and seems to be stuck at 32 permutations. Is this duration expected? In a previous run with 500 permutations, the runtime was 5 hours. I am also running it with the “none” algorithm, which 5000 permutations which is already running for 3 hours and is a 7%.
Would you have an idea why this might take so long or how to optimize the performance to make the process run faster.
Command:
connectomestats \
-tfce_dh 0.1 \
-tfce_e 0.5 \
-tfce_h 2.5 \
-nshuffles 5000 \
-debug \
-force \
/fred/oz251/Arla/derivatives/LA/mrtrix/NBS/DH/mrtrix_bindirectional_connectome/file_name_list.txt \
tfnbs \
/fred/oz251/Arla/derivatives/LA/mrtrix/NBS/DH/design_matrix/Design_without_covariates.txt \
/fred/oz251/Arla/derivatives/LA/mrtrix/NBS/DH/design_matrix/Contrast_without_covariates.txt \
/fred/oz251/Arla/derivatives/LA/mrtrix/NBS/tfnbs_output_withoutCovariats_super
Design:
1 0 4.78 0.53 -0.76
1 0 1.82 0.53 7.24
1 0 6.68 -0.47 8.24
1 0 -1.95 0.53 -14.76
1 0 -1.74 -0.47 2.24
1 0 5.97 0.53 3.24
1 0 -0.26 0.53 5.24
1 0 -1.43 0.53 0.24
1 0 1.23 -0.47 6.24
1 0 -4.08 -0.47 3.24
1 0 -3.61 0.53 3.24
1 0 4.72 0.53 0.24
1 0 3.30 -0.47 7.24
1 0 -2.92 -0.47 -0.76
1 0 -6.37 0.53 -15.76
1 0 6.64 -0.47 6.24
1 0 -5.82 0.53 -1.76
1 0 1.51 0.53 -12.76
1 0 1.65 -0.47 -8.76
1 0 7.51 0.53 5.24
1 0 7.79 -0.47 2.24
1 0 2.87 0.53 1.24
1 0 4.35 -0.47 2.24
1 0 -5.76 -0.47 5.24
1 0 1.38 0.53 -1.76
1 0 -3.93 0.53 -12.76
1 0 -4.35 0.53 -14.76
1 0 -6.76 -0.47 -4.76
1 0 1.36 -0.47 -8.76
1 0 -0.83 0.53 -8.76
1 0 -1.91 -0.47 -2.76
1 0 -2.55 -0.47 6.24
1 0 5.14 -0.47 1.24
1 0 -0.60 0.53 3.24
1 0 3.76 -0.47 -9.76
1 0 -6.27 -0.47 -11.76
1 0 -6.77 0.53 -13.76
1 0 -1.65 -0.47 1.24
1 0 7.82 -0.47 7.24
1 0 -3.75 0.53 5.24
1 0 8.01 -0.47 0.24
1 0 -1.69 -0.47 -6.76
1 0 3.91 -0.47 8.24
1 0 5.19 -0.47 -1.76
1 0 -1.82 0.53 -10.76
1 0 -0.93 0.53 1.24
1 0 2.83 0.53 -1.76
1 0 6.33 -0.47 -4.76
1 0 11.56 -0.47 -10.76
1 0 2.59 0.53 -10.76
1 0 -4.45 0.53 3.24
1 0 -1.49 0.53 -4.76
1 0 10.80 -0.47 -1.76
1 0 3.96 0.53 7.24
1 0 -6.41 0.53 -2.76
1 0 -4.22 0.53 5.24
1 0 -2.48 0.53 -0.76
0 1 -12.05 0.53 7.24
0 1 -10.91 0.53 0.04
0 1 -3.95 0.53 8.24
0 1 5.06 -0.47 -4.76
0 1 -1.20 -0.47 0.24
0 1 -3.17 0.53 -4.76
0 1 4.08 -0.47 -12.76
0 1 -13.59 -0.47 -7.76
0 1 0.49 0.53 1.24
0 1 -1.84 -0.47 12.24
0 1 4.22 -0.47 11.24
0 1 -3.84 -0.47 0.24
0 1 -7.00 0.53 1.24
0 1 -0.68 0.53 8.24
0 1 -9.96 0.53 -1.76
0 1 2.46 -0.47 -2.76
0 1 -7.11 0.53 5.24
0 1 -6.58 -0.47 8.24
0 1 -7.75 0.53 1.24
0 1 0.05 -0.47 2.24
0 1 -0.74 -0.47 0.04
0 1 -1.77 -0.47 2.24
0 1 1.19 -0.47 0.04
0 1 11.48 -0.47 -1.76
0 1 -2.37 -0.47 -7.76
0 1 1.83 -0.47 8.24
0 1 -2.19 -0.47 0.24
0 1 4.35 0.53 1.24
0 1 -8.20 -0.47 0.04
0 1 -3.15 -0.47 -4.76
0 1 4.75 -0.47 9.24
0 1 -7.42 -0.47 5.24
0 1 5.28 0.53 6.24
0 1 -1.82 -0.47 -3.76
0 1 -2.13 -0.47 1.24
0 1 3.49 0.53 8.24
0 1 -4.32 -0.47 1.24
0 1 8.36 -0.47 -12.76
0 1 -8.70 0.53 12.24
0 1 2.78 0.53 9.24
0 1 7.42 0.53 -6.76
0 1 7.75 -0.47 9.24
0 1 8.54 -0.47 5.24
0 1 6.80 -0.47 -2.76
0 1 0.84 0.53 3.24
0 1 2.55 0.53 8.24
Contrast:
1 -1 0 0 0
Thank you!
Lizanne