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Dear experts,
I used the function fspalm to run permutations with the following options: fspalm --glmdir /my_glmdir/ --cft 1.3 --name palm --iters 10000 --cwp .05 --onetail
Checking the palmcofig.txt file that is generated as output, I realized that even if the "–logp" flag wasn't specified in the function, this flag is always applied with fspalm, and therefore the p-values of the *dpv_tstat_uncp.mgz file are saved as -log10(p). Consequently, if I want to threshold with p, I must first convert these values to p-values using 10^(- p) and then use p<0.05.
In contrast, when I load the files *dpv _tstat_fwep.mgz and *clustere_tstat_fwep.mgz, the results don't appear to be -log10(p), and then these files wouldn't need to be transformed with 10^(- p) to use a threshold of p<0.05.
What is the use of this flag in fspalm and why does it only affect the uncorrected p values?
Thank you in advance. Marina
This is more of a question for the PALM developer (whom I have cc'ed).
On 5/19/2021 8:15 AM, Marina Fernández wrote:
External Email - Use Caution
Dear experts,
I used the function fspalm to run permutations with the following options: fspalm --glmdir /my_glmdir/ --cft 1.3 --name palm --iters 10000 --cwp .05 --onetail
Checking the palmcofig.txt file that is generated as output, I realized that even if the "–logp" flag wasn't specified in the function, this flag is always applied with fspalm, and therefore the p-values of the *dpv_tstat_uncp.mgz file are saved as -log10(p). Consequently, if I want to threshold with p, I must first convert these values to p-values using 10^(- p) and then use p<0.05.
In contrast, when I load the files *dpv _tstat_fwep.mgz and *clustere_tstat_fwep.mgz, the results don't appear to be -log10(p), and then these files wouldn't need to be transformed with 10^(- p) to use a threshold of p<0.05.
What is the use of this flag in fspalm and why does it only affect the uncorrected p values?
Thank you in advance. Marina
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Marina Fernández