Failure to detect entorhinal grid-like signals in a passive navigation human fMRI study.
The 2 matches
- [1] § Results › Unimodal signal interference ↔ Analyses_GridLikeSignals.R, lines 319–373 · score 0.54 · behavioural task scores, fold signal, predicted, magnitude, Unimodal, hemisphere
- [2] § Methods › Statistical analyses ↔ Analyses_GridLikeSignals.R, lines 319–373 · score 0.51 · behavioral task, GLS magnitudes, scoring, hemisphere, Welch, fold
Paper
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The authors' code
R · 373 lines · 13 KB · MIT · 2 matches
- # grid_analysis.R
- # Analysis script for Kransberg et al. (2025) - GLS fMRI Study
- # Author: Jonas Kransberg
- # Date last modified: 02.05.2025
- # Author contact information: [email hidden]
- # 0. Load required libraries
- library(tidyverse)
- library(lmerTest)
- # 1. Generate dummy data
- set.seed(123)
- # 1.1 Create participant-level info for manual segmentation
- n_manual <- 110
- manual_ids <- factor(1:n_manual)
- participant_manual <- tibble(
- subject_id = manual_ids,
- visit_age = runif(n_manual, 16, 80),
- subject_sex = factor(sample(c("Male","Female"), n_manual, replace = TRUE)),
- total_correct_combined = sample(1:7, n_manual, replace = TRUE)
- ) %>%
- mutate(
- age_group = factor(ifelse(visit_age < 40, "Under40", "Above40"),
- levels = c("Under40","Above40"))
- )
- # 1.2 Expand to row-level for manual segmentation
- manual <- expand_grid(
- participant_manual,
- segmentation = "manual_segmentation",
- xfoldsym = c(1,5,6,7),
- roi = factor(c("rh_erc","lh_erc")),
- smoothing = c(0,4)
- ) %>%
- mutate(
- beta_gridcode_mean_combined = rnorm(n(), 0, 0.1),
- rayleigh_z = runif(n(), 0, 1), # spatial stability metric
- temporally_stable = runif(n(), 0, 100) # temporal stability metric (percent)
- )
- # 1.3 Create participant-level info for automatic segmentation
- n_auto <- 207
- auto_ids <- factor(1:n_auto)
- participant_auto <- tibble(
- subject_id = auto_ids,
- visit_age = runif(n_auto, 18.2, 78.6),
- subject_sex = factor(sample(c("Male","Female"), n_auto, replace = TRUE)),
- total_correct_combined = sample(1:7, n_auto, replace = TRUE)
- ) %>%
- mutate(
- age_group = factor(ifelse(visit_age < 40, "Under40", "Above40"),
- levels = c("Under40","Above40"))
- )
- automatic <- expand_grid(
- participant_auto,
- segmentation = "automatic_segmentation",
- xfoldsym = c(1,5,6,7),
- roi = factor(c("rh_erc","lh_erc")),
- smoothing = c(0,4)
- ) %>%
- mutate(
- beta_gridcode_mean_combined = rnorm(n(), 0, 0.1)
- )
- # Combine datasets
- combined <- bind_rows(manual, automatic)
- # 2. Grid-Like Signal (GLS) Analyses
- ## 2.1 6-Fold GLS vs Zero
- for(region in c("rh_erc","lh_erc")){
- cat("6-fold GLS vs zero in", region, "\n")
- print(t.test(filter(manual, xfoldsym==6, roi==region, smoothing == 0)$beta_gridcode_mean_combined,
- mu=0, alternative = "greater", na.rm = TRUE))
- }
- ## 2.2 Control Symmetry Checks (5- and 7-fold)
- for(sym in c(5,7)){
- for(region in c("rh_erc","lh_erc")){
- cat(sym, "-fold GLS vs zero in", region, "\n")
- print(t.test(filter(manual, xfoldsym==sym, roi==region, smoothing == 0)$beta_gridcode_mean_combined,
- mu=0, alternative = "greater", na.rm = TRUE))
- }
- }
- ## 2.3 Age-Group Stratification (<40 vs ≥40)
- ### Younger group (<40)
- for(sym in c(6,5,7)){
- for(region in c("rh_erc","lh_erc")){
- cat("Younger (<40):", sym, "-fold GLS vs zero in", region, "\n")
- data_y <- filter(manual, age_group=="Under40", xfoldsym==sym, roi==region, smoothing == 0)
- print(t.test(data_y$beta_gridcode_mean_combined, mu=0, alternative = "greater", na.rm = TRUE))
- }
- }
- ### Older group (≥40)
- for(sym in c(6,5,7)){
- for(region in c("rh_erc","lh_erc")){
- cat("Older (≥40):", sym, "-fold GLS vs zero in", region, "\n")
- data_o <- filter(manual, age_group=="Above40", xfoldsym==sym, roi==region, smoothing == 0)
- print(t.test(data_o$beta_gridcode_mean_combined, mu=0, alternative = "greater", na.rm = TRUE))
- }
- }
- ## 2.4 Between-Group Comparison for 6-Fold
- for(region in c("rh_erc","lh_erc")){
- cat("Between-group Welch t-test for 6-fold in", region, "\n")
- dt <- filter(manual, xfoldsym==6, roi==region, smoothing == 0)
- print(t.test(beta_gridcode_mean_combined ~ age_group, data=dt, alternative = "greater"))
- }
- ## 2.5 Continuous Age Effects (LME)
- model_6f <- lmer(beta_gridcode_mean_combined ~ visit_age * roi + subject_sex +
- (1|subject_id), data = filter(manual, xfoldsym==6, smoothing == 0))
- summary(model_6f)
- # 3. Temporal and Spatial Stability Analyses
- temp <- manual %>%
- filter(xfoldsym == 6, smoothing == 0)
- ## 3.1 Temporal Stability Analyses
- for(region in c("rh_erc","lh_erc")){
- df <- filter(temp, roi == region)
- cat("Temporal stability one-sample t-test in", region, "(H0: mean = 50%)\n")
- print(t.test(df$temporally_stable, mu = 50))
- cat("Temporal stability age-group comparison in", region, "\n")
- print(t.test(temporally_stable ~ age_group, data = df))
- }
- ## 3.2 Spatial Stability Analyses
- # Using Rayleigh's Z, test age-group differences
- for(region in c("rh_erc","lh_erc")){
- df <- filter(temp, roi == region)
- cat("Spatial stability age-group t-test for rayleigh_z in", region, "\n")
- print(t.test(rayleigh_z ~ age_group, data = df))
- }
- # 4 Control Analyses: Smoothing
- ## 4.1 6-Fold GLS vs Zero
- for(region in c("rh_erc","lh_erc")){
- cat("6-fold GLS vs zero in", region, "\n")
- print(t.test(filter(manual, xfoldsym==6, roi==region, smoothing == 4)$beta_gridcode_mean_combined,
- mu=0))
- }
- ## 4.2 Control Symmetry Checks (5- and 7-fold)
- for(sym in c(5,7)){
- for(region in c("rh_erc","lh_erc")){
- cat(sym, "-fold GLS vs zero in", region, "\n")
- print(t.test(filter(manual, xfoldsym==sym, roi==region, smoothing == 4)$beta_gridcode_mean_combined,
- mu=0))
- }
- }
- ## 4.3 Age-Group Stratification (<40 vs ≥40)
- ### Younger group (<40)
- for(sym in c(6,5,7)){
- for(region in c("rh_erc","lh_erc")){
- cat("Younger (<40):", sym, "-fold GLS vs zero in", region, "\n")
- data_y <- filter(manual, age_group=="Under40", xfoldsym==sym, roi==region, smoothing == 4)
- print(t.test(data_y$beta_gridcode_mean_combined, mu=0))
- }
- }
- ### Older group (≥40)
- for(sym in c(6,5,7)){
- for(region in c("rh_erc","lh_erc")){
- cat("Older (≥40):", sym, "-fold GLS vs zero in", region, "\n")
- data_o <- filter(manual, age_group=="Above40", xfoldsym==sym, roi==region, smoothing == 4)
- print(t.test(data_o$beta_gridcode_mean_combined, mu=0))
- }
- }
- ## 4.4 Between-Group Comparison for 6-Fold
- for(region in c("rh_erc","lh_erc")){
- cat("Between-group Welch t-test for 6-fold in", region, "\n")
- dt <- filter(manual, xfoldsym==6, roi==region, smoothing == 4)
- print(t.test(beta_gridcode_mean_combined ~ age_group, data=dt))
- }
- ## 4.5 Correlate GLS by smoothing type
- manualsmoothing_rh <- manual %>%
- filter(xfoldsym == 6, roi == "rh_erc") %>%
- select(subject_id, smoothing, beta_gridcode_mean_combined) %>%
- pivot_wider(names_from = smoothing,
- values_from = beta_gridcode_mean_combined,
- names_prefix = "smoothing_")
- cor.test(manualsmoothing_rh$smoothing_0, manualsmoothing_rh$smoothing_4)
- manualsmoothing_lh <- manual %>%
- filter(xfoldsym == 6, roi == "lh_erc") %>%
- select(subject_id, smoothing, beta_gridcode_mean_combined) %>%
- pivot_wider(names_from = smoothing,
- values_from = beta_gridcode_mean_combined,
- names_prefix = "smoothing_")
- cor.test(manualsmoothing_lh$smoothing_0, manualsmoothing_lh$smoothing_4)
- # 5 Control Analyses: Segmentation
- #Re-do primary analyses with automatically segmented EC masks.
- ## 5.1 6-Fold GLS vs Zero
- for(region in c("rh_erc","lh_erc")){
- cat("6-fold GLS vs zero in", region, "\n")
- print(t.test(filter(automatic, xfoldsym==6, roi==region, smoothing == 0)$beta_gridcode_mean_combined,
- mu=0))
- }
- ## 5.2 Control Symmetry Checks (5- and 7-fold)
- for(sym in c(5,7)){
- for(region in c("rh_erc","lh_erc")){
- cat(sym, "-fold GLS vs zero in", region, "\n")
- print(t.test(filter(automatic, xfoldsym==sym, roi==region, smoothing == 0)$beta_gridcode_mean_combined,
- mu=0))
- }
- }
- ## 5.3 Age-Group Stratification (<40 vs ≥40)
- ### Younger group (<40)
- for(sym in c(6,5,7)){
- for(region in c("rh_erc","lh_erc")){
- cat("Younger (<40):", sym, "-fold GLS vs zero in", region, "\n")
- data_y <- filter(automatic, age_group=="Under40", xfoldsym==sym, roi==region, smoothing == 0)
- print(t.test(data_y$beta_gridcode_mean_combined, mu=0))
- }
- }
- ### Older group (≥40)
- for(sym in c(6,5,7)){
- for(region in c("rh_erc","lh_erc")){
- cat("Older (≥40):", sym, "-fold GLS vs zero in", region, "\n")
- data_o <- filter(automatic, age_group=="Above40", xfoldsym==sym, roi==region, smoothing == 0)
- print(t.test(data_o$beta_gridcode_mean_combined, mu=0))
- }
- }
- ## 5.4 Between-Group Comparison for 6-Fold
- for(region in c("rh_erc","lh_erc")){
- cat("Between-group Welch t-test for 6-fold in", region, "\n")
- dt <- filter(automatic, xfoldsym==6, roi==region, smoothing == 0)
- print(t.test(beta_gridcode_mean_combined ~ age_group, data=dt))
- }
- ## 5.5 Correlate GLS by smoothing type
- # Right hemisphere
- combinedcorrh <- combined %>%
- filter(xfoldsym == 6, roi == "rh_erc", smoothing == 0) %>%
- select(subject_id, segmentation, beta_gridcode_mean_combined) %>%
- pivot_wider(names_from = segmentation,
- values_from = beta_gridcode_mean_combined,
- names_prefix = "seg_")
- cor.test(combinedcorrh$seg_manual_segmentation, combinedcorrh$seg_automatic_segmentation)
- # Left hemisphere
- combinedcorlh <- combined %>%
- filter(xfoldsym == 6, roi == "lh_erc", smoothing == 0) %>%
- select(subject_id, segmentation, beta_gridcode_mean_combined) %>%
- pivot_wider(names_from = segmentation,
- values_from = beta_gridcode_mean_combined,
- names_prefix = "seg_")
- cor.test(combinedcorlh$seg_manual_segmentation, combinedcorlh$seg_automatic_segmentation)
- # 6 High-Performance Participants Analysis
- ## 6. 1 Behavioral Performance Ceiling Effects
- behavrh <- manual %>% filter(xfoldsym == 6, roi == "rh_erc", smoothing == 0)
- behavlh <- manual %>% filter(xfoldsym == 6, roi == "lh_erc", smoothing == 0)
- table(behavrh$age_group, behavrh$total_correct_combined >= 6)
- ## 6.2 Age-Group Difference in Task Scores
- print(t.test(total_correct_combined ~ age_group, data=behavrh))
- ## 6.3 GLS After Excluding Low Scorers (<=6)
- high_perf <- filter(manual, total_correct_combined >= 6)
- ## 6.4 6-Fold GLS vs Zero
- for(region in c("rh_erc","lh_erc")){
- cat("6-fold GLS vs zero in", region, "\n")
- print(t.test(filter(high_perf, xfoldsym==6, roi==region, smoothing == 0)$beta_gridcode_mean_combined,
- mu=0))
- }
- ## 6.5 Control Symmetry Checks (5- and 7-fold)
- for(sym in c(5,7)){
- for(region in c("rh_erc","lh_erc")){
- cat(sym, "-fold GLS vs zero in", region, "\n")
- print(t.test(filter(high_perf, xfoldsym==sym, roi==region, smoothing == 0)$beta_gridcode_mean_combined,
- mu=0))
- }
- }
- ## 6.6 Age-Group Stratification (<40 vs ≥40)
- ### Younger group (<40)
- for(sym in c(6,5,7)){
- for(region in c("rh_erc","lh_erc")){
- cat("Younger (<40):", sym, "-fold GLS vs zero in", region, "\n")
- data_y <- filter(high_perf, age_group=="Under40", xfoldsym==sym, roi==region, smoothing == 0)
- print(t.test(data_y$beta_gridcode_mean_combined, mu=0))
- }
- }
- ### Older group (≥40)
- for(sym in c(6,5,7)){
- for(region in c("rh_erc","lh_erc")){
- cat("Older (≥40):", sym, "-fold GLS vs zero in", region, "\n")
- data_o <- filter(high_perf, age_group=="Above40", xfoldsym==sym, roi==region, smoothing == 0)
- print(t.test(data_o$beta_gridcode_mean_combined, mu=0))
- }
- }
- ## 6.7 Between-Group Comparison for 6-Fold
- for(region in c("rh_erc","lh_erc")){
- cat("Between-group Welch t-test for 6-fold in", region, "\n")
- dt <- filter(high_perf, xfoldsym==6, roi==region, smoothing == 0)
- print(t.test(beta_gridcode_mean_combined ~ age_group, data=dt))
- }
- ## 6.8 Correlation Analyses
- # Behavioural task scores and Age
- print(cor.test(behavrh$visit_age, behavrh$total_correct_combined))
- # Behavioural task scores and GLS magnitude
- # Right hemisphere
- print(cor.test(behavrh$beta_gridcode_mean_combined, behavrh$total_correct_combined))
- # Left hemisphere
- print(cor.test(behavlh$beta_gridcode_mean_combined, behavlh$total_correct_combined))
- # 7. Unimodal (1-Fold) Signal Analyses
- ## 7.1 1-Fold Signal vs Behavior
- filtered <- manual %>% filter(smoothing == 0)
- #rh_cor
- print(cor.test(filter(filtered, xfoldsym==1, roi == "rh_erc")$beta_gridcode_mean_combined,
- filter(filtered, xfoldsym==1, roi == "rh_erc")$total_correct_combined))
- #lh_cor
- print(cor.test(filter(filtered, xfoldsym==1, roi == "lh_erc")$beta_gridcode_mean_combined,
- filter(filtered, xfoldsym==1, roi == "lh_erc")$total_correct_combined))
- ## 7.2 1-Fold Signal
- lme_1f <- lmer(beta_gridcode_mean_combined ~ visit_age * roi + subject_sex +
- (1|subject_id), data = filter(filtered, xfoldsym==1))
- summary(lme_1f)
- ## 7.3 1-Fold Predicting 7-Fold & 6-Fold
- wide <- manual %>%
- filter(smoothing == 0) %>%
- select(subject_id, roi, xfoldsym, beta_gridcode_mean_combined, visit_age) %>%
- pivot_wider(
- names_from = xfoldsym,
- names_prefix = "fold_",
- values_from = beta_gridcode_mean_combined
- )
- lme_1v7 <- lmer(fold_7 ~
- fold_1 * roi + visit_age +
- (1|subject_id), data=wide)
- summary(lme_1v7)
- lme_1v6 <- lmer(fold_6 ~
- fold_1 * roi + visit_age +
- (1|subject_id), data=wide)
- summary(lme_1v6)
Analyses_GridLikeSignals.R at commit de7a08f, under MIT · at the source
Overview
- Center for Lifespan Changes in Brain and Cognition, Department of Psychology, University of Oslo, Norway
- Department of Physics, University of Oslo, Oslo, Norway
- Computational Radiology and Artificial Intelligence, Department of Radiology and Nuclear Medicine, Oslo University Hospital, Oslo, Norway
- Department of Biomedical Engineering and Department of Psychological & Brain Sciences, Center for Systems Neuroscience, Cognitive Neuroimaging Center, Neurophotonics Center, Boston University, Boston, MA, United States
- Department of Neurosurgery, Boston Medical Center, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, United States
- Center for Behavioral Brain Sciences (CBBS), Magdeburg, Germany
- Aging, Cognition & Technology Research Group, German Center for Neurodegenerative Diseases (DZNE), Magdeburg, Germany
Abstract
Grid cells in the human entorhinal cortex (EC) play a critical role in spatial navigation and memory. The EC is also one of the first regions affected by ageing and Alzheimer’s disease. This pre-registered functional magnetic resonance imaging (fMRI) study aimed to detect grid-cell-like signals (GLS) in a passive virtual navigation task. Contrary to our hypotheses and previous findings, we did not observe significant GLS at a population level, even in younger participants. Further exploratory analyses investigated the impact of task-engagement, as inferred from object-location memory performance, and showed no relationship with GLS magnitude. We also examined potential influences of a confounding one-fold directional signal and various data-processing choices but observed no consistent patterns. Our findings, consistent with recent null results from similar studies, suggest that passive navigation paradigms may be insufficient for reliably eliciting grid-like signals in human fMRI.
Reproduced under the paper's license (CC BY), from the paper cited above.
Repository
Its files are read in the Code ↔ Paper reader above, with 2 matches between paragraphs and lines of code.
jokran/GLS_fMRI_Analysis_Kransberg_2025
de7a08fd0593e7f7645913ff16899121b0473fc3, 2 May 2025Availability: 1 check, the latest on 29 September 2026: the link answers
- 29 September 2026: the link answers
3 files
- Analyses_GridLikeSignals
.R — R, 373 lines, 2 matches - LICENSE — License, 21 lines
- README.md — Text, 36 lines
The paper's code and data availability statement is in the Data section.
Tracing map
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What the map holds:
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- 1 script, each with its path and the digest of its content;
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Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.
Data
No dataset and no data link were found in the paper.
Data and Code Availability
The study pre-registration can be found at https://
Reproduced under the paper's license (CC BY), from the paper cited above.
Versions
The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.
Version 1, 29 September 2026: the first record
Recorded: type, language, journal, volume, pages, dates, 10 authors, 5 keywords, 2 funders, 55 references.
Cite
This paper
Kransberg, J., Sjøli Bråthen, A. C., Falch, E. S., Øverbye, K. E., Garrido, P. F., Fjell, A. M., Stangl, M., Wolbers, T., Sneve, M. H., & Walhovd, K. B. (2026). Failure to detect entorhinal grid-like signals in a passive navigation human fMRI study. Imaging neuroscience (Cambridge, Mass.), 4, IMAG.a.1196. https://
BibTeX
@article{kransberg2026fa
author = {Kransberg, Jonas and Sjøli Bråthen, Anne Cecilie and Falch, Emilie Sogn and Øverbye, Knut E.Ø. and Garrido, Pablo F. and Fjell, Anders M. and Stangl, Matthias and Wolbers, Thomas and Sneve, Markus H. and Walhovd, Kristine B.},
title = {{Failure to detect entorhinal grid-like signals in a passive navigation human fMRI study}},
journal = {Imaging neuroscience (Cambridge, Mass.)},
year = {2026},
month = apr,
volume = {4},
pages = {IMAG.a.1196},
publisher = {MIT Press},
issn = {2837-6056},
doi = {10.1162/
url = {https://
pmid = {41958631},
pmcid = {PMC13058850}
}
RIS
TY - JOUR
AU - Kransberg, Jonas
AU - Sjøli Bråthen, Anne Cecilie
AU - Falch, Emilie Sogn
AU - Øverbye, Knut E.Ø.
AU - Garrido, Pablo F.
AU - Fjell, Anders M.
AU - Stangl, Matthias
AU - Wolbers, Thomas
AU - Sneve, Markus H.
AU - Walhovd, Kristine B.
TI - Failure to detect entorhinal grid-like signals in a passive navigation human fMRI study
T2 - Imaging neuroscience (Cambridge, Mass.)
J2 - Imaging Neurosci (Camb)
PY - 2026
DA - 2026/
VL - 4
SP - IMAG.a.1196
SN - 2837-6056
PB - MIT Press
DO - 10.1162/
UR - https://
LA - en
ER -
CSL-JSON
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"container-title": "Imaging neuroscience (Cambridge, Mass.)",
"author": [
{
"family": "Kransberg",
"given": "Jonas"
},
{
"family": "Sjøli Bråthen",
"given": "Anne Cecilie"
},
{
"family": "Falch",
"given": "Emilie Sogn"
},
{
"family": "Øverbye",
"given": "Knut E.Ø."
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{
"family": "Garrido",
"given": "Pablo F."
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{
"family": "Fjell",
"given": "Anders M."
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{
"family": "Stangl",
"given": "Matthias"
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{
"family": "Wolbers",
"given": "Thomas"
},
{
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"given": "Markus H."
},
{
"family": "Walhovd",
"given": "Kristine B."
}
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"container-title-short":
"volume": "4",
"page": "IMAG.a.1196",
"DOI": "10.1162/
"PMID": "41958631",
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"ISSN": "2837-6056",
"publisher": "MIT Press",
"URL": "https://
"language": "en",
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"date-parts": [
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}
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- Rapid formation of non-spatial hippocampal representations consistent with behavioral timescale synaptic plasticity is modulated by entorhinal input.Journal: Nature communicationsIn common: 4 references
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