# \#statistics **URL:** https://mne.discourse.group/tag/statistics/35.md [Latest](https://mne.discourse.group/latest.md) · [Categories](https://mne.discourse.group/categories.md) · [Tags](https://mne.discourse.group/tags.md) --- ## [Channel adjacency for EEG data](https://mne.discourse.group/t/channel-adjacency-for-eeg-data/11672)
**Author:** [@Alx-mor](https://mne.discourse.group/u/Alx-mor)\ **Replies:** 5\ **Last updated:** [January 26, 2026, 2:09am UTC](https://mne.discourse.group/t/channel-adjacency-for-eeg-data/11672 "2026-01-26T02:09:08Z")
I was running spatio\_temporal\_cluster\_1samp\_test on my EEG data and noticed differences in results with and without adjacency. Initially I used this code to compute adjacency, as it doesn’t exist in get\_builtin\_ch\_adjac… --- ## [Cluster statistics on temporal generalization analysis ouput](https://mne.discourse.group/t/cluster-statistics-on-temporal-generalization-analysis-ouput/4488)
**Author:** [@anapesq](https://mne.discourse.group/u/anapesq)\ **Replies:** 3\ **Last updated:** [December 2, 2025, 1:16pm UTC](https://mne.discourse.group/t/cluster-statistics-on-temporal-generalization-analysis-ouput/4488 "2025-12-02T13:16:03Z")
Dear all, I have implemented temporal generalization analysis following the mne example: https://mne.tools/dev/auto\_examples/decoding/decoding\_time\_generalization\_conditions.html I now have for each participant a matr… --- ## [Contrasted TFR issue after TFCE permutation test](https://mne.discourse.group/t/contrasted-tfr-issue-after-tfce-permutation-test/11552)
**Author:** [@Raspail](https://mne.discourse.group/u/Raspail)\ **Replies:** 0\ **Last updated:** [October 28, 2025, 10:17am UTC](https://mne.discourse.group/t/contrasted-tfr-issue-after-tfce-permutation-test/11552 "2025-10-28T10:17:52Z")
MNE version: 1.7.1 Python version : 3.12 Operating system: Win10 Hello everyone, I’m currently performing a time-frequency analysis on EEG data with a within-subject design (19 participants, two conditions: pre-TMS a… --- ## [Calculate source space clustering with 1 time point](https://mne.discourse.group/t/calculate-source-space-clustering-with-1-time-point/11456)
**Author:** [@Christian](https://mne.discourse.group/u/Christian)\ **Replies:** 1\ **Last updated:** [September 4, 2025, 11:00am UTC](https://mne.discourse.group/t/calculate-source-space-clustering-with-1-time-point/11456 "2025-09-04T11:00:12Z")
Hello MNE community, I am working with source localization in surface EEG. I used LCMV and eLORETA and want to compare two specific time points of the Source Estimates between two conditions. I explored different altern… --- ## [Walkthrough for paired permutation cluster test needed](https://mne.discourse.group/t/walkthrough-for-paired-permutation-cluster-test-needed/11468)
**Author:** [@Cathaway](https://mne.discourse.group/u/Cathaway)\ **Replies:** 2\ **Last updated:** [September 2, 2025, 9:43pm UTC](https://mne.discourse.group/t/walkthrough-for-paired-permutation-cluster-test-needed/11468 "2025-09-02T21:43:23Z")
This issue has been brought up different times as people on this forum try to do permutation tests. My issue in particular is that I find the API doc and tutorial to be extremely confusing, to the extent that I have no i… --- ## [MNE permutation cluster test](https://mne.discourse.group/t/mne-permutation-cluster-test/11438)
**Author:** [@ShahrzadAyoubipour](https://mne.discourse.group/u/ShahrzadAyoubipour)\ **Replies:** 3\ **Last updated:** [August 21, 2025, 1:06am UTC](https://mne.discourse.group/t/mne-permutation-cluster-test/11438 "2025-08-21T01:06:51Z")
Hello! I have 3 groups of participants. PD ON medication, PD OFF medication, and Healthy control (PD group are same participants but 2 different conditions). I plan to run paired cluster permutation between PD ON and P… --- ## [Possibility of obtaining \`adjacency\` from a distance matrix](https://mne.discourse.group/t/possibility-of-obtaining-adjacency-from-a-distance-matrix/11200)
**Author:** [@duodenum](https://mne.discourse.group/u/duodenum)\ **Replies:** 4\ **Last updated:** [May 21, 2025, 9:25am UTC](https://mne.discourse.group/t/possibility-of-obtaining-adjacency-from-a-distance-matrix/11200 "2025-05-21T09:25:31Z")
MNE version: 1.9.0 operating system: Ubuntu 22.04 Hello, Is it possible to obtain the adjacency variable going into permutation cluster tests from a simple distance matrix? A minimal example would be, import numpy as… --- ## [Cluster permutation statistics for PAC](https://mne.discourse.group/t/cluster-permutation-statistics-for-pac/11138)
**Author:** [@bonokat](https://mne.discourse.group/u/bonokat)\ **Replies:** 2\ **Last updated:** [May 8, 2025, 1:03am UTC](https://mne.discourse.group/t/cluster-permutation-statistics-for-pac/11138 "2025-05-08T01:03:56Z")
MNE version: 1.8.0 operating system:Windows 10 Hi All, I am trying to run permutation cluster stats on my phase-amplitude coupling (PAC) data and having some issues with implementation. My data structure: pac\_all - … --- ## [Strategies for controlling dimensions in multiple comparison correction](https://mne.discourse.group/t/strategies-for-controlling-dimensions-in-multiple-comparison-correction/11115)
**Author:** [@Sebastian](https://mne.discourse.group/u/Sebastian)\ **Replies:** 1\ **Last updated:** [April 22, 2025, 1:32pm UTC](https://mne.discourse.group/t/strategies-for-controlling-dimensions-in-multiple-comparison-correction/11115 "2025-04-22T13:32:00Z")
Dear Experts and Colleagues, In my recent research, I encountered a statistical issue: in an initial exploratory MEG analysis, I performed analyses for the entire frequency bands of delta, theta, alpha, beta, gamma1, an… --- ## [Non-parametric cluster-level Wilcoxon](https://mne.discourse.group/t/non-parametric-cluster-level-wilcoxon/5631)
**Author:** [@YakimS](https://mne.discourse.group/u/YakimS)\ **Replies:** 4\ **Last updated:** [April 14, 2025, 2:59pm UTC](https://mne.discourse.group/t/non-parametric-cluster-level-wilcoxon/5631 "2025-04-14T14:59:28Z")
I want to perform a Non-parametric 1 sample cluster statistic on single trial power to find a significant cluster in a within-subject design. Is there a way to perform permutation\_cluster\_1samp\_test with Wilcoxon instea… --- ## [FDR-correction for percentile-threshold of dSPM values](https://mne.discourse.group/t/fdr-correction-for-percentile-threshold-of-dspm-values/10642)
**Author:** [@brizzen](https://mne.discourse.group/u/brizzen)\ **Replies:** 0\ **Last updated:** [December 18, 2024, 2:25pm UTC](https://mne.discourse.group/t/fdr-correction-for-percentile-threshold-of-dspm-values/10642 "2024-12-18T14:25:30Z")
Hi everybody :slight\_smile: I wanted to try out an approach described by Hagberg et al., 2019 where they calculated percentile thresholds using false discovery rate (FDR) corrections for dSPM values. Question: Does it … --- ## [Seeking Guidance on Statistical Tests for SEEG Analysis with MNE](https://mne.discourse.group/t/seeking-guidance-on-statistical-tests-for-seeg-analysis-with-mne/9148)
**Author:** [@const](https://mne.discourse.group/u/const)\ **Replies:** 3\ **Last updated:** [August 2, 2024, 2:02pm UTC](https://mne.discourse.group/t/seeking-guidance-on-statistical-tests-for-seeg-analysis-with-mne/9148 "2024-08-02T14:02:41Z")
Hi everyone, I’ve recently been working with SEEG data in MNE, focusing primarily on (generalized linear model) GLM analysis. However, I have some uncertainties regarding the statistical tests applicable to my analysis,… --- ## [Spatio-temporal custer permutation with linear regression](https://mne.discourse.group/t/spatio-temporal-custer-permutation-with-linear-regression/9073)
**Author:** [@eort](https://mne.discourse.group/u/eort)\ **Replies:** 2\ **Last updated:** [July 18, 2024, 10:09am UTC](https://mne.discourse.group/t/spatio-temporal-custer-permutation-with-linear-regression/9073 "2024-07-18T10:09:57Z")
Hi all, In my MEG project, I want to run a linear regression across sensors and time and combine it with cluster-based permutation to control for multiple comparisons. Based on a few tutorials I managed to write some co… --- ## [spatio\_temporal\_cluster\_1samp : data should be normalized?](https://mne.discourse.group/t/spatio-temporal-cluster-1samp-data-should-be-normalized/9009)
**Author:** [@LeilaNS](https://mne.discourse.group/u/LeilaNS)\ **Replies:** 1\ **Last updated:** [June 28, 2024, 9:20am UTC](https://mne.discourse.group/t/spatio-temporal-cluster-1samp-data-should-be-normalized/9009 "2024-06-28T09:20:04Z")
Hi, I want to use spatio\_temporal\_cluster\_1samp\_test(X, n\_permutations=n\_permutations, threshold=t\_threshold, n\_jobs=3, tail=1, seed=34). My X data consists of n\_subjects, all magnetometer sensors, and 48 epochs. The sh… --- ## [Clarification of factor\_levels in f\_rm\_mway](https://mne.discourse.group/t/clarification-of-factor-levels-in-f-rm-mway/8956)
**Author:** [@duodenum](https://mne.discourse.group/u/duodenum)\ **Replies:** 0\ **Last updated:** [June 19, 2024, 6:09am UTC](https://mne.discourse.group/t/clarification-of-factor-levels-in-f-rm-mway/8956 "2024-06-19T06:09:00Z")
MNE version: 1.7.0 operating system: openSUSE Leap 42.3 Hello, I am trying to understand how f\_rm\_mway figures out the factors in the design. I have a task design where I have two factors, one of them has 3 levels an… --- ## [How to plot the results of the permutation\_cluster\_test for labels](https://mne.discourse.group/t/how-to-plot-the-results-of-the-permutation-cluster-test-for-labels/7394)
**Author:** [@Kate](https://mne.discourse.group/u/Kate)\ **Replies:** 1\ **Last updated:** [May 24, 2024, 1:31pm UTC](https://mne.discourse.group/t/how-to-plot-the-results-of-the-permutation-cluster-test-for-labels/7394 "2024-05-24T13:31:27Z")
Hello all, Can you please give me some advice, I used permutation\_cluster\_test for source sLORETA time courses. I extracted activity from a few labels. Now my data looks like number of observations \* time points \* ROI… --- ## [TFCE Exponent Values](https://mne.discourse.group/t/tfce-exponent-values/8709)
**Author:** [@sb\_mnml](https://mne.discourse.group/u/sb_mnml)\ **Replies:** 1\ **Last updated:** [April 25, 2024, 2:02pm UTC](https://mne.discourse.group/t/tfce-exponent-values/8709 "2024-04-25T14:02:37Z")
MNE version: 1.6.0 operating system: Windows 10 Hi there, When using TFCE for permutation cluster testing, is there a way to change the h and e exponent values from the defaults? I’ve checked the documentation but co… --- ## [Reduce memroy usage for permutation\_cluster\_test with TFCE](https://mne.discourse.group/t/reduce-memroy-usage-for-permutation-cluster-test-with-tfce/8486)
**Author:** [@NIcolasFT](https://mne.discourse.group/u/NIcolasFT)\ **Replies:** 1\ **Last updated:** [March 16, 2024, 7:46am UTC](https://mne.discourse.group/t/reduce-memroy-usage-for-permutation-cluster-test-with-tfce/8486 "2024-03-16T07:46:47Z")
Hi all, In the current implementation (MNE 1.6.1 and current main on github), the use of TFCE in permutation\_cluster\_test uses a lot of memory. This make it totally unpracticable between 2D data (like time frequency map… --- ## [Max number of electrodes spatio-temporal clusters](https://mne.discourse.group/t/max-number-of-electrodes-spatio-temporal-clusters/8245)
**Author:** [@Catsine](https://mne.discourse.group/u/Catsine)\ **Replies:** 1\ **Last updated:** [February 19, 2024, 10:24am UTC](https://mne.discourse.group/t/max-number-of-electrodes-spatio-temporal-clusters/8245 "2024-02-19T10:24:39Z")
Hi! I have a question about the spatio-temporal cluster permutation method applied in mne. Is it possible to establish a maximum number of electrodes to consider in each cluster as done in FieldTrip? Thanks! --- ## [How to use cluster permutation on eeg data? Question about seed, stat\_fun,and others](https://mne.discourse.group/t/how-to-use-cluster-permutation-on-eeg-data-question-about-seed-stat-fun-and-others/8323)
**Author:** [@Xiang\_F\_Y](https://mne.discourse.group/u/Xiang_F_Y)\ **Replies:** 0\ **Last updated:** [February 13, 2024, 4:21pm UTC](https://mne.discourse.group/t/how-to-use-cluster-permutation-on-eeg-data-question-about-seed-stat-fun-and-others/8323 "2024-02-13T16:21:50Z")
MNE version: 1.6.1\_0 operating system: macOS(M3) I have some questions about the usage of permutation\_cluster\_test. I am working on EEG source space connectivity data from MATLAB. I have two condition data from 38 sub… --- ## [sampling procedure in combination with ANOVA & spatio-temporal permutation test for unbalanced data](https://mne.discourse.group/t/sampling-procedure-in-combination-with-anova-spatio-temporal-permutation-test-for-unbalanced-data/8306)
**Author:** [@coderb](https://mne.discourse.group/u/coderb)\ **Replies:** 0\ **Last updated:** [February 9, 2024, 7:51am UTC](https://mne.discourse.group/t/sampling-procedure-in-combination-with-anova-spatio-temporal-permutation-test-for-unbalanced-data/8306 "2024-02-09T07:51:25Z")
Hello everyone! I’m running a two-way ANOVA on sensor-level spatiotemporal data (evoked responses) and correcting for multiple comparisons with cluster-based permutation tests. This is my code: def stat\_fun(\*args): … --- ## [Cluster-based permutation test for a 2x3 Design](https://mne.discourse.group/t/cluster-based-permutation-test-for-a-2x3-design/7991)
**Author:** [@brizzen](https://mne.discourse.group/u/brizzen)\ **Replies:** 0\ **Last updated:** [December 12, 2023, 12:30pm UTC](https://mne.discourse.group/t/cluster-based-permutation-test-for-a-2x3-design/7991 "2023-12-12T12:30:53Z")
Hi everyone, I am trying to compute statistics on ERP-Data (32 Channels x 720 time-points) for a 2-by-3 design. Following this tutorial (Mass-univariate twoway repeated measures ANOVA on single trial power — MNE 1.6.0 d… --- ## [Default value of stim\_dur in make\_first\_level\_design\_matrix function (fNIRS)](https://mne.discourse.group/t/default-value-of-stim-dur-in-make-first-level-design-matrix-function-fnirs/7162)
**Author:** [@YaeletK](https://mne.discourse.group/u/YaeletK)\ **Replies:** 1\ **Last updated:** [December 6, 2023, 4:22pm UTC](https://mne.discourse.group/t/default-value-of-stim-dur-in-make-first-level-design-matrix-function-fnirs/7162 "2023-12-06T16:22:48Z")
Hi, I am trying to figure out if there is a way to use my conditions stimulation times and durations (they are not all the same) from the annotations of the raw (hemoglobin) file, instead of using a set defined length t… --- ## [Extract Confidence Interval](https://mne.discourse.group/t/extract-confidence-interval/7963)
**Author:** [@NeuroPhdStud](https://mne.discourse.group/u/NeuroPhdStud)\ **Replies:** 1\ **Last updated:** [December 6, 2023, 10:47am UTC](https://mne.discourse.group/t/extract-confidence-interval/7963 "2023-12-06T10:47:49Z")
Hello everyone, I am new to EEG preprocessing and till now I managed to get my evoked potentials. However, they seem a little noisy and therefore I wanted to check if the components I observe are really existing or not… --- ## [Cluster permutation statistics.](https://mne.discourse.group/t/cluster-permutation-statistics/7526)
**Author:** [@Nikita13021995](https://mne.discourse.group/u/Nikita13021995)\ **Replies:** 0\ **Last updated:** [September 14, 2023, 1:25pm UTC](https://mne.discourse.group/t/cluster-permutation-statistics/7526 "2023-09-14T13:25:08Z")
MNE version: 1.4.2 operating system: Windows 10 Dear collegues, We are computing permutation statistics for mne\_connectivity by using the function: conpy.cluster\_permutation\_test (more or less equal to mne.stats.perm… --- ## [Statistical tests for connectivity measures](https://mne.discourse.group/t/statistical-tests-for-connectivity-measures/7295)
**Author:** [@lokinou](https://mne.discourse.group/u/lokinou)\ **Replies:** 1\ **Last updated:** [August 3, 2023, 8:02pm UTC](https://mne.discourse.group/t/statistical-tests-for-connectivity-measures/7295 "2023-08-03T20:02:54Z")
It’s more a methods and mathematical question rather than a pure software question. I have one participant with about 500x 2 second epochs of EEG data with 64channels in two difference sessions, let’s call them PRE and … --- ## [TFCE clustering using the t-values from LME models (and how to modify the stat\_fun param)](https://mne.discourse.group/t/tfce-clustering-using-the-t-values-from-lme-models-and-how-to-modify-the-stat-fun-param/7301)
**Author:** [@polomoro](https://mne.discourse.group/u/polomoro)\ **Replies:** 0\ **Last updated:** [July 27, 2023, 4:36pm UTC](https://mne.discourse.group/t/tfce-clustering-using-the-t-values-from-lme-models-and-how-to-modify-the-stat-fun-param/7301 "2023-07-27T16:36:05Z")
Dear all, I’ve been analysing the MEG data from 50 participants to study the correlations between the brain oscillations in some frequency bands and their behaviour during a task. For each participant, I extracted 23 ep… --- ## [spatio\_temporal\_cluster\_test with NaNs in data](https://mne.discourse.group/t/spatio-temporal-cluster-test-with-nans-in-data/4926)
**Author:** [@M055](https://mne.discourse.group/u/M055)\ **Replies:** 5\ **Last updated:** [June 9, 2023, 3:59pm UTC](https://mne.discourse.group/t/spatio-temporal-cluster-test-with-nans-in-data/4926 "2023-06-09T15:59:12Z")
Hey all, new to MNE, and trying to use MNE’s spatio\_temporal\_cluster\_test for some fNIRS data that has been separately processed using personal scripts (i.e., not using MNE etc). As part of the pre-processing stage, ar… --- ## [creating the permutation null distribution](https://mne.discourse.group/t/creating-the-permutation-null-distribution/6917)
**Author:** [@anapesq](https://mne.discourse.group/u/anapesq)\ **Replies:** 4\ **Last updated:** [May 19, 2023, 9:24am UTC](https://mne.discourse.group/t/creating-the-permutation-null-distribution/6917 "2023-05-19T09:24:29Z")
Hello, I am trying to use mne.stats.permutation\_cluster\_1samp\_test to run a non-parametric cluster based statistics. However, instead of letting the mne function create the permutated timeseries to compose the estimated… --- ## [Loading preprocessed EEG data for statistical analyses in MNE](https://mne.discourse.group/t/loading-preprocessed-eeg-data-for-statistical-analyses-in-mne/6486)
**Author:** [@Nils27](https://mne.discourse.group/u/Nils27)\ **Replies:** 2\ **Last updated:** [May 12, 2023, 8:44am UTC](https://mne.discourse.group/t/loading-preprocessed-eeg-data-for-statistical-analyses-in-mne/6486 "2023-05-12T08:44:02Z")
Hi all, I am new to MNE and was wondering if it is possible to load already preprocessed EEG data in MNE to do some sophisticated statistical analysis like non-parametric permutation statistics. In more detail, I did a … [Next page](https://mne.discourse.group/tag/statistics/35.md?match_all_tags=true&page=1&tags%5B%5D=statistics)