Multimodal laminar characterization of visual areas along the cortical hierarchy.
The 14 matches · 5 of them tie a paragraph to a whole file, not to given lines: weak matches, whose lines are not tinted
- [1] § Materials and Methods › Statistical analysis on microscopy laminar profiles ↔ AHEAD/04_Laminar_profiles/12_compue_stats.py, lines 44–86 · score 0.80 · Wilcoxon signed rank, Bonferroni correction, post hoc, ANOVA, laminar profiles, correlation
- [2] § Results › Comparing the microscopic cortical architecture of visual areas ↔ AHEAD/04_Laminar_profiles/12_compue_stats.py, lines 44–86 · score 0.80 · Wilcoxon signed rank, Bonferroni correction, post hoc, Pairwise comparisons, ANOVA, correlates
- [3] § Materials and Methods › Data acquisition › In-vivo MRI dataset ↔ stimulus_scripts/hMT_Localiser/Main/MQ_locMt_Huk_AP.py, lines 1–43 · score 0.77 · fixation cross, Siemens, slab, GE, localizer, scanning
- [4] § Materials and Methods › Cortical mapping › Tissue segmentation ↔ AHEAD/05_qMRI/03_ants_registration.sh, the whole file · a weak match · score 0.67 · rim polish, qMRI, ITK, smoothing, global, voronoi
- [5] § Materials and Methods › Cortical mapping › Region-of-interest definition ↔ Anat/4_create_subcorticalMask.sh, the whole file · a weak match · score 0.62 · subcortical masking, BrainVoyager, ACPC, hemisphere, UNI, Segmentation
- [6] § Materials and Methods › Data acquisition › In-vivo MRI dataset ↔ stimulus_scripts/MotionQuartet/ambiguous.py, lines 1–48 · score 0.58 · pulses, fMRI, scanning, stimuli, distance, TR
- [7] § Materials and Methods › Data preprocessing for laminar signal extraction › Post-mortem dataset › Microscopy data › Intensity normalization ↔ AHEAD/04_Laminar_profiles/00_polish_2D_slices.py, lines 38–87 · score 0.57 · outer gray matter, deviations, kernel, thickness, slice, Filter
- [8] § Materials and Methods › Data preprocessing for laminar signal extraction › Post-mortem dataset › Microscopy data › Intensity normalization ↔ AHEAD/03_post_CBA/optional_to_polish_segmentation/2D_final_polishing.py, lines 26–67 · score 0.57 · outer gray matter, deviations, kernel, thickness, Filter, voxel
- [9] § Materials and Methods › Data acquisition › Post-mortem dataset ↔ AHEAD/05_qMRI/01_extractROI.py, lines 12–25 · score 0.57 · proton density, qMRI, R1, reconstructed, ROI, brain
- [10] § Materials and Methods › Data preprocessing for laminar signal extraction › In-vivo dataset › Resting-state fMRI ↔ fMRI_Processing/LOC/1_preprocessFMR.py, lines 10–41 · score 0.55 · high pass filter, motion correction, preprocessing, temporal, slice
- [11] § Materials and Methods › Cortical mapping › Region-of-interest definition ↔ Anat/2_read_VMR_export_nifti.py, lines 1–13 · score 0.52 · subcortical masking, BrainVoyager, Pipeline, anatomical
- [12] § Materials and Methods › Data preprocessing for laminar signal extraction › In-vivo dataset › Anatomical MRI ↔ fMRI_Processing/PRF/02_ants_apply_registration_tseries.sh, the whole file · a weak match · score 0.52 · transformation matrix, co registration, resampled, echo, MRI
- [13] § Materials and Methods › Geometric cortical layers ↔ AHEAD/05_qMRI/cutting_effect/02_compute_streamlines.sh, the whole file · a weak match · score 0.51 · LN2_LAYERS, Cutting Angle, computational, equivol, segmentation
- [14] § Materials and Methods › Data preprocessing for laminar signal extraction › In-vivo dataset › Resting-state fMRI ↔ in_vivo_qMRI/resting_state/Preprocessing/03_read_fmr_export_nifti.py, the whole file · a weak match · score 0.50 · motion correction, BrainVoyager, TOPUP, preprocessing, slice, resolution
Paper
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The authors' code
Python · 86 lines · 4 KB · no license · 2 matches
- import numpy as np
- import pandas as pd
- from scipy.stats import shapiro, friedmanchisquare, f_oneway
- from scipy.stats import wilcoxon
- # Step 1: Data input
- data = {
- 'Region Pair': ['V1-V2', 'V1-V3', 'V2-V3', 'V1-hMT+', 'V2-hMT+', 'V3-hMT+',
- 'V1-V2', 'V1-V3', 'V2-V3', 'V1-hMT+', 'V2-hMT+', 'V3-hMT+'],
- 'Hemisphere': ['Left', 'Left', 'Left', 'Left', 'Left', 'Left', 'Right', 'Right', 'Right', 'Right', 'Right',
- 'Right'],
- 'Bielschowsky': [0.994, 0.997, 0.996, 0.993, 0.995, 0.996, 0.999, 0.993, 0.996, 0.998, 0.998, 0.995],
- 'Thionin': [0.994, 0.985, 0.996, 0.961, 0.963, 0.948, 0.999, 0.998, 0.999, 0.988, 0.989, 0.989],
- 'Parvalbumin': [0.997, 0.989, 0.991, 0.942, 0.921, 0.917, 0.995, 0.978, 0.974, 0.938, 0.925, 0.981]
- }
- df = pd.DataFrame(data)
- # Step 2: Fisher Z-transformation
- def fisher_z_transform(r):
- return 0.5 * np.log((1 + r) / (1 - r))
- df['Bielschowsky_Z'] = df['Bielschowsky'].apply(fisher_z_transform)
- df['Thionin_Z'] = df['Thionin'].apply(fisher_z_transform)
- df['Parvalbumin_Z'] = df['Parvalbumin'].apply(fisher_z_transform)
- # Step 3: Compute descriptive statistics (means and standard deviations)
- means = df[['Bielschowsky_Z', 'Thionin_Z', 'Parvalbumin_Z']].mean()
- std_devs = df[['Bielschowsky_Z', 'Thionin_Z', 'Parvalbumin_Z']].std()
- print("Means:\n", means)
- print("\nStandard Deviations:\n", std_devs)
- # Step 4: Check for normality with Shapiro-Wilk test
- _, p_biel = shapiro(df['Bielschowsky_Z'])
- _, p_thio = shapiro(df['Thionin_Z'])
- _, p_parv = shapiro(df['Parvalbumin_Z'])
- print("\nShapiro-Wilk p-values:")
- print(f"Bielschowsky: {p_biel}, Thionin: {p_thio}, Parvalbumin: {p_parv}")
- # Step 5: Perform the appropriate statistical test
- # If normal, run ANOVA
- if p_biel > 0.05 and p_thio > 0.05 and p_parv > 0.05:
- print("\nData is normally distributed. Running ANOVA...")
- F_stat, p_anova = f_oneway(df['Bielschowsky_Z'], df['Thionin_Z'], df['Parvalbumin_Z'])
- print(f"ANOVA result: F = {F_stat}, p = {p_anova}")
- # Post-hoc analysis (if significant)
- if p_anova < 0.05:
- print("Significant result, performing post-hoc analysis...")
- print("Pairwise comparisons using Wilcoxon signed-rank test (non-parametric post-hoc)...")
- _, p_b_t = wilcoxon(df['Bielschowsky_Z'], df['Thionin_Z'])
- _, p_b_p = wilcoxon(df['Bielschowsky_Z'], df['Parvalbumin_Z'])
- _, p_t_p = wilcoxon(df['Thionin_Z'], df['Parvalbumin_Z'])
- print(f"Bielschowsky vs Thionin: p = {p_b_t}")
- print(f"Bielschowsky vs Parvalbumin: p = {p_b_p}")
- print(f"Thionin vs Parvalbumin: p = {p_t_p}")
- # Apply Bonferroni correction (multiply p-values by 3)
- p_b_t_corr = min(p_b_t * 3, 1.0) # Ensure that the corrected p-value is <= 1
- p_b_p_corr = min(p_b_p * 3, 1.0)
- p_t_p_corr = min(p_t_p * 3, 1.0)
- # Print corrected p-values
- print(f"Bielschowsky vs Thionin: p (uncorrected) = {p_b_t}, p (Bonferroni corrected) = {p_b_t_corr}")
- print(f"Bielschowsky vs Parvalbumin: p (uncorrected) = {p_b_p}, p (Bonferroni corrected) = {p_b_p_corr}")
- print(f"Thionin vs Parvalbumin: p (uncorrected) = {p_t_p}, p (Bonferroni corrected) = {p_t_p_corr}")
- # If not normal, run Friedman test
- else:
- print("\nData is not normally distributed. Running Friedman test...")
- stat, p_friedman = friedmanchisquare(df['Bielschowsky_Z'], df['Thionin_Z'], df['Parvalbumin_Z'])
- print(f"Friedman result: chi-square = {stat}, p = {p_friedman}")
- # Post-hoc analysis (if significant)
- if p_friedman < 0.05:
- print("Significant result, performing post-hoc analysis...")
- print("Pairwise comparisons using Wilcoxon signed-rank test (non-parametric post-hoc)...")
- _, p_b_t = wilcoxon(df['Bielschowsky_Z'], df['Thionin_Z'])
- _, p_b_p = wilcoxon(df['Bielschowsky_Z'], df['Parvalbumin_Z'])
- _, p_t_p = wilcoxon(df['Thionin_Z'], df['Parvalbumin_Z'])
- print(f"Bielschowsky vs Thionin: p = {p_b_t}")
- print(f"Bielschowsky vs Parvalbumin: p = {p_b_p}")
- print(f"Thionin vs Parvalbumin: p = {p_t_p}")
12_compue_stats.py at commit 90b326d, no license · at the source
Overview
- Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, Netherlands
- Brain Innovation B.V., Maastricht, Netherlands
- Full brain picture Analytics, Leiden, Netherlands
- Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
Abstract
Understanding how brain structure gives rise to function remains a central challenge in neuroscience. Post-mortem histology provides unparalleled microstructural insight into cytoarchitecture, myeloarchitecture, and cell-type distributions, yet lacks information on functional coupling. Conversely, in-vivo MRI can reveal functional dynamics but with limited microstructural specificity. Bridging these modalities is, therefore, essential for advancing our understanding of cortical organization. Here, we investigate laminar organization across the human visual hierarchy by integrating post-mortem and in-vivo imaging. Specifically, we combined post-mortem histology and quantitative MRI (qMRI) from the Alkemade and colleagues’ dataset (Alkemade et al., 2022) with in-vivo ultra-high resolution q T2* MRI (0.35 mm isotropic) and resting-state layer-fMRI (0.8 mm isotropic), focusing on areas V1, V2, V3, and hMT+. Among post-mortem measures, parvalbumin (PV) interneuron distributions across cortical layers best discriminated visual areas, outperforming cell body density (Nissl) and fiber density (Bielschowsky). Furthermore, comparing laminar R2* profiles across modalities revealed systematic differences between post-mortem and in-vivo MRI, attributable to the absence of vascular contributions in post-mortem data. Extending these laminar analyses to resting-state fMRI acquisition (here only the temporal mean is used for the laminar profiles) represents a first step toward linking structural and functional profiles across layers. Finally, we make our analysis framework publicly available to enable broader exploration of laminar organization across cortical systems using the Alkemade et al. (2022) dataset. This integrative approach sets the stage for future frameworks that unite microstructural and functional data, advancing the development of next-generation models of cortical computation.
Reproduced under the paper's license (CC BY), from the paper cited above.
Repositories
Its files are read in the Code ↔ Paper reader above, with 14 matches between paragraphs and lines of code.
27-apizzuti/multimodal_layers
90b326dbede25de4f8f7d4601ef773ff570712c1, 15 November 2024Availability: 1 check, the latest on 27 September 2026: the link answers
- 27 September 2026: the link answers
72 files
- AHEAD/
01_CBA/ , Python, 44 lines0_intensity_normalizatio n_microscopy.py - AHEAD/
01_CBA/ , Python, 112 lines2_read_nifti_write_vmr.p y - AHEAD/
01_CBA/ , MATLAB, 28 linesatlas_poi_to_average_ste p5.m - AHEAD/
01_CBA/ , MATLAB, 34 linesaverage_poi_to_subject_s tep6.m - AHEAD/
03_post_CBA/ , Python, 30 lines1_read_VMR_export_nifti. py - AHEAD/
03_post_CBA/ , Python, 43 lines2_apply_TRX.py - AHEAD/
03_post_CBA/ , Python, 72 lines3D_final_polishing.py - AHEAD/
03_post_CBA/ , Python, 29 lines3_combine_seg.py - AHEAD/
03_post_CBA/ , Python, 40 lines4_create_RIM.py - AHEAD/
03_post_CBA/ , Python, 28 lines6_reduce_seg.py - AHEAD/
03_post_CBA/ , Python, 84 linescutting_effect/ 03_angles.py - AHEAD/
03_post_CBA/ , Python, 46 linescutting_effect/ 1_extractROI.py - AHEAD/
03_post_CBA/ , Shell, 6 linescutting_effect/ 2_compute_streamlines.sh - AHEAD/
03_post_CBA/ , Python, 78 lines, 1 matchoptional_to_polish_segme ntation/ 2D_final_polishing.py - AHEAD/
03_post_CBA/ , Python, 72 linesoptional_to_polish_segme ntation/ 3D_final_polishing.py - AHEAD/
04_Laminar_profiles/ , Python, 98 lines, 1 match00_polish_2D_slices.py - AHEAD/
04_Laminar_profiles/ , Python, 107 lines01_split_3D_input_in_2D. py - AHEAD/
04_Laminar_profiles/ , Python, 31 lines02_compute_2D_layers.py - AHEAD/
04_Laminar_profiles/ , Python, 38 lines03_propagate_angles.py - AHEAD/
04_Laminar_profiles/ , Python, 62 lines04_stack_3D_midGM_for_dr awing_control_points.py - AHEAD/
04_Laminar_profiles/ , Python, 55 lines05_split_3D_control_poin ts.py - AHEAD/
04_Laminar_profiles/ , Python, 92 lines06_create_UV.py - AHEAD/
04_Laminar_profiles/ , Python, 49 lines07_compute_UVD_FILTER_LP .py - AHEAD/
04_Laminar_profiles/ , Python, 48 lines08_compute_UVD_FILTER_HP .py - AHEAD/
04_Laminar_profiles/ , Python, 45 lines09_correct_bias.py - AHEAD/
04_Laminar_profiles/ , Python, 63 lines10_stack_3D.py - AHEAD/
04_Laminar_profiles/ , Python, 112 lines11_plot_layers.py - AHEAD/
04_Laminar_profiles/ , Python, 86 lines, 2 matches12_compue_stats.py - AHEAD/
04_Laminar_profiles/ , Python, 13 linesmy_layer_profiles.py - AHEAD/
05_qMRI/ , Python, 46 lines, 1 match01_extractROI.py - AHEAD/
05_qMRI/ , Python, 57 lines02_closing_operation_bub ble.py - AHEAD/
05_qMRI/ , Shell, 59 lines, 1 match03_ants_registration.sh - AHEAD/
05_qMRI/ , Python, 98 lines04_polish_2D_slices.py - AHEAD/
05_qMRI/ , Python, 85 lines05_split_3D_input_in_2D. py - AHEAD/
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05_qMRI/ , Python, 102 lines09_plot_layers_PD.py - AHEAD/
05_qMRI/ , Python, 134 lines09_plot_layers_T2star.py - AHEAD/
05_qMRI/ , Shell, 7 linesBrain_extraction.sh - AHEAD/
05_qMRI/ , Shell, 7 lines, 1 matchcutting_effect/ 02_compute_streamlines.s h - AHEAD/
05_qMRI/ , Python, 78 linescutting_effect/ 03_angles.py - AHEAD/
05_qMRI/ , Python, 45 linesmerge_ROIs.py - AHEAD/
05_qMRI/ , Python, 13 linesmy_layer_profiles.py - in_vivo_qMRI/
3D_ME_EPI/ , Python, 121 lines01_read_nifti_write_vmr. py - in_vivo_qMRI/
3D_ME_EPI/ , Python, 95 lines02_prepare_segm_for_surf ace.py - in_vivo_qMRI/
3D_ME_EPI/ , Python, 35 lines03_read_VMR_export_nifti .py - in_vivo_qMRI/
3D_ME_EPI/ , Python, 72 lines04_polishing_segmentatio n/ 3D_final_polishing.py - in_vivo_qMRI/
3D_ME_EPI/ , Python, 32 lines07_clean_cutROIs.py - in_vivo_qMRI/
3D_ME_EPI/ , Python, 94 lines08_plot_layers.py - in_vivo_qMRI/
3D_ME_EPI/ , Python, 110 lines09_plot_layers_R2star.py - in_vivo_qMRI/
3D_ME_EPI/ , Python, 97 lines10_plot_layers_wT2star.p y - in_vivo_qMRI/
3D_ME_EPI/ , Python, 109 lines11_plot_layers_restingSt ate.py - in_vivo_qMRI/
3D_ME_EPI/ , Python, 111 lines12_plot_layers_restingSt ate_aligned.py - in_vivo_qMRI/
3D_ME_EPI/ , Python, 96 lines13_plot_layers_S0.py - in_vivo_qMRI/
3D_ME_EPI/ , MATLAB, 27 linesatlas_poi_to_average_ste p1.m - in_vivo_qMRI/
3D_ME_EPI/ , MATLAB, 33 linesaverage_poi_to_subject_s tep2.m - in_vivo_qMRI/
3D_ME_EPI/ , Python, 13 linesmy_layer_profiles.py - in_vivo_qMRI/
resting_state/ , Python, 36 lines01_fix_header.py - in_vivo_qMRI/
resting_state/ , Shell, 6 lines02_run_greedy_nonlinear. sh - in_vivo_qMRI/
resting_state/ , Python, 111 lines03_plot_layers_restingSt ate_aligned.py - in_vivo_qMRI/
resting_state/ , Python, 40 linesPreprocessing/ 01_preprocessFMR.py - in_vivo_qMRI/
resting_state/ , Python, 61 linesPreprocessing/ 02_create_input_topup.py - in_vivo_qMRI/
resting_state/ , Python, 81 lines, 1 matchPreprocessing/ 03_read_fmr_export_nifti .py - in_vivo_qMRI/
resting_state/ , Python, 51 linesPreprocessing/ 04_run_topup.py - in_vivo_qMRI/
resting_state/ , Python, 59 linesPreprocessing/ 05_apply_topup_tseries.p y - in_vivo_qMRI/
resting_state/ , Python, 57 linesPreprocessing/ 06_fix_fmr_after_topup.p y - in_vivo_qMRI/
resting_state/ , Python, 38 linesPreprocessing/ 07_hpf.py - in_vivo_qMRI/
resting_state/ , Python, 75 linesPreprocessing/ 08_create_VTC_afterBBR.p y - in_vivo_qMRI/
resting_state/ , Python, 45 linesPreprocessing/ 09_adapt_VTC_header.py - in_vivo_qMRI/
resting_state/ , Python, 52 linesPreprocessing/ 10_export_NIFTI_from_VTC .py - README.md, Text, 22 lines
27-apizzuti/meso_motionquartet
4c453809a2d9a15807f087b3781d31e826499849, 4 February 2025Availability: 1 check, the latest on 27 September 2026: the link answers
- 27 September 2026: the link answers
140 files
- Anat/
0_brain_extraction.sh , Shell, 21 lines - Anat/
11_combine_polishedWM_VM , Python, 29 linesR.py - Anat/
12_createCorticalMask_ex , Python, 45 linesport_VMR.py - Anat/
13_convert_voi_nifti.py , Python, 40 lines - Anat/
14_voronoi.sh , Shell, 24 lines - Anat/
15_create_RIM.py , Python, 58 lines - Anat/
16_dilate_ROI.py , Python, 36 lines - Anat/
17_selectRIM_toSegment.s , Shell, 8 linesh - Anat/
18_polish_segmentation.s , Shell, 10 linesh - Anat/
19_final_voronoi.sh , Shell, 29 lines - Anat/
1_VMR_zoom.py , Python, 57 lines - Anat/
20_convert_nifti_to_voi. , Python, 45 linespy - Anat/
21_LN2_LAYERS.py , Python, 37 lines - Anat/
2_read_VMR_export_nifti. , Python, 37 lines, 1 matchpy - Anat/
3_NIFTI_export_VMR.py , Python, 69 lines - Anat/
4_create_subcorticalMask , Shell, 19 lines, 1 match.sh - Anat/
4_read_VMP_export_nifti. , Python, 49 linespy - Anat/
5_apply_mask.py , Python, 47 lines - Anat/
6_polish_one_tissue.py , Python, 46 lines - Anat/
7_WM_nifti_to_VMR.py , Python, 44 lines - Anat/
8_insert_polished_WM.py , Python, 35 lines - Anat/
convert_nifti_to_voi_tem , Python, 43 linesp.py - Anat/
polish_VMR_4figure.py , Python, 30 lines - Anat/
preps/ , Python, 32 lines01_create_anat_VMR.py - Anat/
preps/ , Python, 28 lines02_IIHC_anat_VMR.py - Anat/
preps/ , Python, 39 lines03_read_VMR_export_nifti .py - Anat/
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preps/ , Python, 24 lines05_NIFTI_export_VMR.py - Figures/
01_plot_PHY_AM_betas_com , Python, 87 linesparison.py - Figures/
01r_plot_PHY_AM_betas_co , Python, 93 linesmparison_boxplot.py - Figures/
02_plot_group_layer_prof , Python, 117 linesile_betas_cluster_PHY_AM B.py - Figures/
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extras/ , Python, 96 linesplot_AM_FL_ROI_effect.py - Figures/
extras/ , Python, 117 linesplot_group_layer_profile _betas_cluster_dom_minus _suppressed.py - Figures/
my_layer_profiles.py , Python, 13 lines - MetaScript/
2_allocate_DICOM.py , Python, 57 lines - MetaScript/
4_create_nifti.py , Python, 70 lines - MetaScript/
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LOC/ , Shell, 57 lines01_ants_registration-fun c.sh - fMRI_Processing/
LOC/ , Shell, 22 lines02_ants_apply_registrati on_tseries.sh - fMRI_Processing/
LOC/ , Python, 62 lines0_read_fmr_export_nifti. py - fMRI_Processing/
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MOT_QUARTET/ , Python, 63 linesClustersVisualizationFla t/ 02_MULTILATERATE.py - fMRI_Processing/
MOT_QUARTET/ , Python, 58 linesClustersVisualizationFla t/ 03_UVD_FILTER.py - fMRI_Processing/
MOT_QUARTET/ , Python, 49 linesClustersVisualizationFla t/ 03b_check_disk_coverage. py - fMRI_Processing/
MOT_QUARTET/ , Python, 83 linesClustersVisualizationFla t/ 04_retinotopy_consistenc y_ambiguous.py - fMRI_Processing/
MOT_QUARTET/ , Python, 30 linesClustersVisualizationFla t/ 05_PATCH_FLATTEN_PREPARA TION.py - fMRI_Processing/
MOT_QUARTET/ , Python, 91 linesClustersVisualizationFla t/ 06_PATCH_FLATTEN.py - fMRI_Processing/
MOT_QUARTET/ , Python, 25 linesClustersVisualizationFla t/ 07_ADJUST_OUTPUTNAME.py - fMRI_Processing/
MOT_QUARTET/ , Python, 40 linesClustersVisualizationFla t/ 07_MEDIAN_PROJECTION.py - fMRI_Processing/
MOT_QUARTET/ , Python, 47 linesClustersVisualizationFla t/ 08_MAX_PROJECTION.py - fMRI_Processing/
MOT_QUARTET/ , Python, 47 linesClustersVisualizationFla t/ 09_PHY_AMB_CONG.py - fMRI_Processing/
MOT_QUARTET/ , Python, 120 linesClustersVisualizationFla t/ WIP_compare_clusters_V1. py - fMRI_Processing/
MOT_QUARTET/ , Python, 113 linesEventRelatedAverages/ 01_read_nifti_plot_times eries_carpet.py - fMRI_Processing/
MOT_QUARTET/ , Python, 109 linesEventRelatedAverages/ 02_read_prt_generate_tim eseries_carpet_labels.py - fMRI_Processing/
MOT_QUARTET/ , Python, 76 linesEventRelatedAverages/ 03_generate_trial_labels _for_PRT.py - fMRI_Processing/
MOT_QUARTET/ , Python, 89 linesEventRelatedAverages/ 04_normalize_each_trial. py - fMRI_Processing/
MOT_QUARTET/ , Python, 137 linesEventRelatedAverages/ 05_event_related_average s_per_roi.py - fMRI_Processing/
MOT_QUARTET/ , Python, 122 linesEventRelatedAverages/ 06_group_average_plot_li ne_ERA.py - fMRI_Processing/
MOT_QUARTET/ , Python, 105 linesEventRelatedAverages/ 07_group_average_plot_li ne_dominant_notDominant. py - fMRI_Processing/
MOT_QUARTET/ , Python, 69 linesEventRelatedAverages/ preps/ 00_combine_voi.py - fMRI_Processing/
MOT_QUARTET/ , Python, 61 linesEventRelatedAverages/ preps/ 01_read_vtc_write_nifti. py - fMRI_Processing/
MOT_QUARTET/ , Python, 97 linesEventRelatedAverages/ preps/ 02_read_voi_and_vtc_writ e_nifti.py - fMRI_Processing/
MOT_QUARTET/ , Python, 13 linesmy_layer_profiles.py - fMRI_Processing/
MOT_QUARTET/ , Python, 89 linesplot_motionParameters.py - fMRI_Processing/
PRF/ , Shell, 57 lines01_ants_registration-fun c.sh - fMRI_Processing/
PRF/ , Shell, 39 lines, 1 match02_ants_apply_registrati on_tseries.sh - fMRI_Processing/
PRF/ , Python, 87 lines0_read_fmr_export_nifti. py - fMRI_Processing/
PRF/ , Python, 44 lines10_adapt_VTC_header.py - fMRI_Processing/
PRF/ , Python, 58 lines11_create_input_mapping. py - fMRI_Processing/
PRF/ , Python, 64 lines12_PRF_mapping.py - fMRI_Processing/
PRF/ , Python, 63 lines13_create_VMP.py - fMRI_Processing/
PRF/ , Python, 97 lines13_create_stimulus_mask. py - fMRI_Processing/
PRF/ , Python, 34 lines14_avg_mapping.py - fMRI_Processing/
PRF/ , Python, 65 lines14_read_VMP_export_nifti .py - fMRI_Processing/
PRF/ , Python, 37 lines15_apply_V1_mask.py - fMRI_Processing/
PRF/ , Python, 37 lines16_check_PRF_mask_multil aterateCoverage.py - fMRI_Processing/
PRF/ , Python, 46 lines1_preprocessFMR_prf.py - fMRI_Processing/
PRF/ , Python, 57 lines2_create_input_topup_prf .py - fMRI_Processing/
PRF/ , Python, 69 lines2_read_fmr_export_nifti. py - fMRI_Processing/
PRF/ , Python, 50 lines3_run_topup.py - fMRI_Processing/
PRF/ , Python, 54 lines5_apply_topup_tseries.py - fMRI_Processing/
PRF/ , Python, 37 lines6_hpf.py - fMRI_Processing/
PRF/ , Python, 50 lines7_create_ref_4BBR.py - fMRI_Processing/
PRF/ , Python, 38 lines8_run_BBR.py - fMRI_Processing/
PRF/ , Python, 68 lines9_create_VTC_afterBBR.py - fMRI_Processing/
PRF/ , Python, 72 linesmapping.py - stimulus_scripts/
MotionQuartet/ , Python, 435 lines, 1 matchambiguous.py - stimulus_scripts/
MotionQuartet/ , Python, 443 linesunambiguous.py - stimulus_scripts/
hMT_Localiser/ , Python, 69 linesCode/ CreateConditionsMtLocHuk _4min.py - stimulus_scripts/
hMT_Localiser/ , Python, 662 lines, 1 matchMain/ MQ_locMt_Huk_AP.py - stimulus_scripts/
prf_experiment/ , Python, 28 linesconfig.py - stimulus_scripts/
prf_experiment/ , Python, 161 linesmain.py - stimulus_scripts/
prf_experiment/ , Python, 33 linesmonitor.py - stimulus_scripts/
prf_experiment/ , Python, 59 linesstim.py - stimulus_scripts/
prf_experiment/ , Python, 409 linestasks.py - stimulus_scripts/
prf_experiment/ , Python, 269 linesutils.py - README.md, Text, 15 lines
ofgulban/segmentator
01f46b36152734d67495417528fcc384eb567732, 7 June 2023Availability: 1 check, the latest on 27 September 2026: the link answers
- 27 September 2026: the link answers
24 files
- segmentator/
__init__.py , Python, 5 lines - segmentator/
__main__.py , Python, 184 lines - segmentator/
config.py , Python, 37 lines - segmentator/
config_filters.py , Python, 14 lines - segmentator/
config_gui.py , Python, 13 lines - segmentator/
cython/ , C, 4,388 linesderiche_3D.c - segmentator/
deriche_prepare.py , Python, 42 lines - segmentator/
filter.py , Python, 143 lines - segmentator/
filters_ui.py , Python, 103 lines - segmentator/
filters_utils.py , Python, 134 lines - segmentator/
future/ , Python, 119 lineswip_arcweld_mp2rage.py - segmentator/
future/ , Python, 118 lineswip_arcweld_mprage.py - segmentator/
gui_utils.py , Python, 663 lines - segmentator/
hist2d_counts.py , Python, 31 lines - segmentator/
ncut_prepare.py , Python, 120 lines - segmentator/
segmentator_main.py , Python, 270 lines - segmentator/
segmentator_ncut.py , Python, 242 lines - segmentator/
tests/ , Python, 34 linestest_utils.py - segmentator/
tests/ , Python, 48 lineswip_test_arcweld.py - segmentator/
tests/ , Python, 34 lineswip_test_gradient_magnit ude.py - segmentator/
utils.py , Python, 348 lines - setup.py, Python, 36 lines
- LICENSE, License, 11 lines
- README.md, Text, 67 lines
figshare 26045911
Availability: 1 check, the latest on 27 September 2026: the link answers (HTTP 200)
- 27 September 2026: the link answers (HTTP 200)
The paper's code and data availability statement is in the Data section.
Tracing map
Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.
What the map holds:
- 4 repositories of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
- 232 scripts, each with its path and the digest of its content;
- 14 matches between paragraphs of the paper and lines of the code (method lexical-v1);
- neither the text of the paper nor the code itself.
Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.
Data
Datasets cited
- portal.brain-map.org/
overview , at Allen Brain Map; found in the text, “Extending open access tools for the…” - zenodo:14147820, at Zenodo; found in “Data and Code Availability”
- zenodo:14164885, at Zenodo; found in “Data and Code Availability”
Data and Code Availability
Analysis code is available on GitHub: 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 2, 28 September 2026
- Funding: added H2020 Excellent Science: H2020-860563, 945539
Version 1, 27 September 2026: the first record
Recorded: type, language, journal, volume, pages, dates, 7 authors, 6 keywords, 89 references.
Cite
This paper
Pizzuti, A., Bazin, P.-L., Ivanov, D., Dresbach, S., Peters, J. C., Goebel, R., & Gulban, O. F. (2026). Multimodal laminar characterization of visual areas along the cortical hierarchy. Imaging neuroscience (Cambridge, Mass.), 4, IMAG.a.1279. https://
BibTeX
@article{pizzuti2026mult
author = {Pizzuti, Alessandra and Bazin, Pierre-Louis and Ivanov, Dimo and Dresbach, Sebastian and Peters, Judith C and Goebel, Rainer and Gulban, Omer Faruk},
title = {{Multimodal laminar characterization of visual areas along the cortical hierarchy}},
journal = {Imaging neuroscience (Cambridge, Mass.)},
year = {2026},
month = jul,
volume = {4},
pages = {IMAG.a.1279},
publisher = {MIT Press},
issn = {2837-6056},
doi = {10.1162/
url = {https://
pmid = {42459498},
pmcid = {PMC13370752}
}
RIS
TY - JOUR
AU - Pizzuti, Alessandra
AU - Bazin, Pierre-Louis
AU - Ivanov, Dimo
AU - Dresbach, Sebastian
AU - Peters, Judith C
AU - Goebel, Rainer
AU - Gulban, Omer Faruk
TI - Multimodal laminar characterization of visual areas along the cortical hierarchy
T2 - Imaging neuroscience (Cambridge, Mass.)
J2 - Imaging Neurosci (Camb)
PY - 2026
DA - 2026/
VL - 4
SP - IMAG.a.1279
SN - 2837-6056
PB - MIT Press
DO - 10.1162/
UR - https://
LA - en
ER -
CSL-JSON
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