I have run a one-sample t-test in both randomise and PALM as a quality check.
Commands:
randomise -i int_4D_all.nii.gz -o randomise_cope2 -T -1 -n 5000
palm -i int_4D_all.nii -o palm_cope2 -T -C 3.1 -n 5000 -save1-p
PALM gives many more outputs compared to randomise when running the same test and wanted to clarify the corresponding outputs.
Questions arose concerning the processing and output:
- (a) Is it correct that palm_cope2_vox_tstat_c1 is equivalent to the output randomise_cope2_tstat1 (which represent the raw tstat)? (b) Additionally, would it also be the case that palm_cope2_tfce_fwep_tstat_c1 is comparable to randomise_cope2_tfce_corrp_tstat1 (which represents the corrected p-values for tfce thresholding)?
- Based on my visual comparison, the values at various voxels align for (a) and are similar for (b) but not exact (e.g., 0.337 for randomise_corrp vs. 0.284 for palm_tfce_fwep). This would be presumable given that it underwent permutation testing, correct?
- PALM was exponentially slower than randomise (4 hours vs. 15 minutes). Why is this the case when the inputs and tests conducted are the same?