References

The main reference for PALM is the same as for randomise:

Winkler AM, Ridgway GR, Webster MA, Smith SM, Nichols TE. Permutation inference for the general linear model. NeuroImage, 2014;92:381-397. (Open Access)

For correction across contrasts (option -corrcon), the most detailed reference is:

Alberton BAV, Nichols TE, Gamba HR, Winkler AM. Multiple testing correction over contrasts for brain imaging. Neuroimage. 2020 Mar 19:116760. (Open Access)

For Non-Parametric Combination (NPC; options -npc, -npcmod and -npccon), classical multivariate tests (MANOVA, MANCOVA; option -mv) assessed with permutations, and for correction over modalities and/or contrasts (options -corrmod and -corrcon), the reference is:

Winkler AM, Webster MA, Brooks JC, Tracey I, Smith SM, Nichols TE. Non-Parametric Combination and related permutation tests for neuroimaging. Hum Brain Mapp. 2016 Apr;37(4):1486-511. (Open Access)

For the multi-level exchangeability blocks (options -eb, -vg, and for HCP data), the reference is:

Winkler AM, Webster MA, Vidaurre D, Nichols TE, Smith SM. Multi-level block permutation. Neuroimage. 2015;123:253-68. (Open Access)

For the accelerated permutation inference (options -accel or -approx), the reference is:

Winkler AM, Ridgway GR, Douaud G, Nichols TE, Smith SM. Faster permutation inference in brain imaging. Neuroimage. 2016 Jun 7;141:502-516. (Open Access)

For the false discovery rate (FDR) approach used in PALM (option -fdr), the reference is:

Winkler AM, Taylor PA, Nichols TE, Rorden C. False Discovery Rate and Localizing Power. arXiv, 2024;2401.03554. (Preprint)

For additional theory of permutation tests in neuroimaging, please see and cite:

Nichols TE, Holmes AP. Nonparametric permutation tests for functional neuroimaging: a primer with examples. Hum Brain Mapp. 2002 Jan;15(1):1-25.

Holmes AP, Blair RC, Watson JD, Ford I. Nonparametric analysis of statistic images from functional mapping experiments. J Cereb Blood Flow Metab. 1996 Jan;16(1):7-22.