I am confused by how randomise determines the number of permutations it will perform.
Randomise is currently running as part of dual_regression over 53 fMRI scans. I specified a maximum of 5000 permutations, yet when I examined the logs I found that only 53 permutations were performed.
Even stranger, running randomise from the command line with the same parameters produced the expected number of permutations for some (but not all) of the components. I examined the dr_stage2_ic files in fslview and there were no obvious issues.
What is going on?
$ cat drD.o22851.10
randomise options: -i /home/nucifora/comp/melodic/redo/dualreg/n5000_20180320011258/dr_stage2_ic0009 -o /home/nucifora/comp/melodic/redo/dualreg/n5000_20180320011258/dr_stage3_ic0009 -m /home/nucifora/comp/melodic/redo/dualreg/n5000_20180320011258/mask -d /home/nucifora/comp/melodic/redo/dualreg/n5000_20180320011258/design.mat -t /home/nucifora/comp/melodic/redo/dualreg/n5000_20180320011258/design.con -n 5000 -T -V
Loading Data:
Data loaded
53 permutations required for exhaustive test of t-test 1
Doing all 53 unique permutations
Starting permutation 1 (Unpermuted data)
Starting permutation 2
Starting permutation 3
$ randomise -i /home/nucifora/comp/melodic/redo/dualreg/n5000_20180320011258/dr_stage2_ic0009 -o /home/nucifora/comp/melodic/redo/dualreg/test-dr_stage3_ic0019 -m /home/nucifora/comp/melodic/redo/dualreg/n5000_20180320011258/mask -d /home/nucifora/comp/melodic/redo/dualreg/n5000_20180320011258/design.mat -t /home/nucifora/comp/melodic/redo/dualreg/n5000_20180320011258/design.con -n 5000 -T -V
randomise options: -i /home/nucifora/comp/melodic/redo/dualreg/n5000_20180320011258/dr_stage2_ic0009 -o /home/nucifora/comp/melodic/redo/dualreg/test-dr_stage3_ic0019 -m /home/nucifora/comp/melodic/redo/dualreg/n5000_20180320011258/mask -d /home/nucifora/comp/melodic/redo/dualreg/n5000_20180320011258/design.mat -t /home/nucifora/comp/melodic/redo/dualreg/n5000_20180320011258/design.con -n 5000 -T -V
Loading Data:
Data loaded
2756 permutations required for exhaustive test of t-test 1
Doing all 2756 unique permutations
Starting permutation 1 (Unpermuted data)
Starting permutation 2
Starting permutation 3
$ randomise -i /home/nucifora/comp/melodic/redo/dualreg/n5000_20180320011258/dr_stage2_ic0019 -o /home/nucifora/comp/melodic/redo/dualreg/test-dr_stage3_ic0019 -m /home/nucifora/comp/melodic/redo/dualreg/n5000_20180320011258/mask -d /home/nucifora/comp/melodic/redo/dualreg/n5000_20180320011258/design.mat -t /home/nucifora/comp/melodic/redo/dualreg/n5000_20180320011258/design.con -n 5000 -T -V
randomise options: -i /home/nucifora/comp/melodic/redo/dualreg/n5000_20180320011258/dr_stage2_ic0019 -o /home/nucifora/comp/melodic/redo/dualreg/test-dr_stage3_ic0019 -m /home/nucifora/comp/melodic/redo/dualreg/n5000_20180320011258/mask -d /home/nucifora/comp/melodic/redo/dualreg/n5000_20180320011258/design.mat -t /home/nucifora/comp/melodic/redo/dualreg/n5000_20180320011258/design.con -n 5000 -T -V
Loading Data:
Data loaded
53 permutations required for exhaustive test of t-test 1
Doing all 53 unique permutations
Starting permutation 1 (Unpermuted data)
Starting permutation 2
Starting permutation 3
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