DOI: 10.5281/zenodo.17476529
title: Data for: Axonal Structure-Function relationships across experimental modalities

description: Data for: "Axonal Structure-Function relationships across experimental modalities"

by

Christian S. Skoven (1,2), Mariam Andersson (1), Miren Lur Barquin Torre (1), Marco Pizzolato (3,1), Hartwig R. Siebner (1,4,5) and Tim B. Dyrby (1,3)

(1) Danish Research Centre for Magnetic Resonance,    Department for Radiology and Nuclear Medicine,    Copenhagen University Hospital Amager and Hvidovre, Copenhagen, Denmark.

(2) Center of Functionally Integrative Neuroscience,    Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.    Technical University of Denmark, Denmark.

(4)    Department of Neurology, Copenhagen University Hospital Bispebjerg and Frederiksberg,    Copenhagen, Denmark.

(5) Department of Clinical Medicine, Faculty of Medical and Health Sciences,    University of Copenhagen, Denmark.

Correspondence:

Christian S. Skoven (cskoven@drcmr.dk) and Tim B. Dyrby (timd@drcmr.dk)

Cryo-TEM

Cryo-TEM images and segmentations from punctures of the anterior midbody in a mid-sagittal slice of 4 rats. Further README-files are present in the subfolders.

Epon-TEM

Epon-TEM raw images (e.g. “20220209_CFIM_TEM”) at 4200x magnification, and corresponding segmentations (e.g. "20220722_ADS_cleaned_manualrefinement)from punctures of the anterior midbody in a mid-sagittal slice of 5 rats. Further README-files are present in the subfolders.

MRI

MRI data for 8 rats.

Scans

May contain some or all of the following:• structural MRI file (*T2_TRUE_FISP*.nii)• dMRI file for AxonDiameter estimation (*DtiStandard_TE36_50dw_b7_19_21-25.nii)• b-vector information for the dMRI file for the AxonDiameter estimation (DtiStandard_TE36_50dw_b7_19_21-25_effbvector.txt)• dMRI for Tractography (*DtiStandard_TE37_b4_Whole.nii)• b-vector information for the dMRI file for the AxonDiameter estimation (DtiStandard_TE37_b4_Whole_effbvector.txt)• Adjusted b-vector information (for proper tractograms) for the dMRI file for the AxonDiameter estimation (nXnYZ_DtiStandard_TE37_b4_Whole_effbvector.txt)

The presence of the following folders depend on whether the raw data was acquired for that particular subject.

ROIs

Contains the ROIS relevant for generating the two tractograms in the “Tracts”-folder.• Seed ROIs: *InjectROI*.nii and *TargetROI*.nii• Target and termination ROI: *ccROI.nii• Exclude ROIs to focus the streamline propagation: *ExcludeROI*.nii

Tracts

• Tractogram files from the left (*Target*.tck) and right (*Inject*.tck) hemisphere projecting through Corpus Callosum and terminating in the mid-sagittal slice.

Maps

• Tractogram maps (corresponding to the Tractogram files in the “Tracts”-folder) indicating the voxels which the tract streamlines passed through.

Results

Contains results files from the dMRI preprocessing:• mask.nii• Preprocessed dMRI data for Tractography: *gn*.mif

and from the tractography process - used to make the tractograms:• Peaks*.nii• respons*.txt• FOD*.mif

May also contain a denoised dMRI file used for AxonDiameter estimation, reoriented to align with the tractography dMRI file.• *_2tract_DWI_DG_averaged.nii.gz

AxonDiameters

• The stitched (left + right) tractograms (from the “Maps”-folder) to extract diameters: tractAxonROI.nii.gz• The AxonDiameter estimate file: diameters_*.nii (fitted from the “*_2tract_DWI_DG_averaged.nii.gz”-file in the “Results”-folder).

Opto-ElPhys

Contains:• Surgery dates for all animals: “SurgDates.csv”• Information about which electrophysiology recording sessions (one session per animal) were used: “AllRats_OneSession.csv”

TranscallosalConductionTime

dfP_20221024-172352.csv

The extracted detected peak latencies for the P1-peak. Has the following information semicolon-separated:• Subject name (“Rat”)• SurgeryDate (“SurgDate”)• Recording Session (“Session”)• Data Preprocessing mode (“Mode”)• Laser Power (“LP”)• Stimulation Duration: (“StimDur”)• Interval for automatic peak detection (“sigOI_start” and “sigOI_end”)• Interpolated “PeakStart” in ms- if detected• Recording value at the interpolated peakStart (“PeakStartVal”) - if detected• Latency of the P1 peak in ms (“Peak”) - if detected• Prominence of the P1 peak (recording value) “PeakVal” at the peak - if detected• Indication of detection satisfaction after manual inspection (“check”)• The number of days between surgery and experiment date (“Delta”)

Log_20221122-174620_CoV_Filtered.csv

The extracted P1 peak latencies extracted from dfP*.csv based on “check=True” and a Coefficient of Variation (“CoV”) for the N1-peak being < 1.0.

TCT_latencies_20210212-170852.png

A plot indicating the peak latency values for both the P1 peak, N1 onset and N1 peak - for all rats. The little subscript next to the marker (e.g.~2, 9 and 9 for rat27.1) indicates how many of the conditions of the stimulation parameter combinations (LP x StimDur) was included for the subject. Only manually inspected automatic peak detections were included, and only when the CoV of the N1 peak was < 1.0.

TrialsRaw_20201229_AllRats:

Contains the extracted trials from the recording raw files (based on the stimulation trigger) for all rats.The trialsRaw-files have the following information in their filename:• trialsRaw_rat27.2_20190625_p06_ADC4_02.0mW_10.0ms.npy• Subject name: “rat27.2”• Session date: “202190625”• Stimulation paradigm number: “p06”• Recording channel: ADC4• Laser Power: “02.0mW”• Stimulation Duration: “10.0ms”Each trial has a length of 1.8s (900 ms pre and post stimulation) The sample rate for the recording is 30kHz. For some animals the 150 trials per conditionmight be found in separate paradigm-files - to spread them out throughout the experiment session. A Jupyter Notebook for basic loading of the trials (“Load_trialsRaw.ipynb”) can be found at: https://gitlab.com/cskoven/opto-elphys

 

Citation:

If you use (parts of) this data, please cite this repository:

Skoven, C. S., Andersson, M., Barquin Torre, M. L., Pizzolato, M., Siebner, H., & Dyrby, T. B. (2025). Data for: Axonal Structure-Function relationships across experimental modalities [Data set]. Zenodo. https://doi.org/10.5281/zenodo.17476529

AND the corresponding peer-reviewed publication:

Skoven CS, Andersson M, Torre MLB, Pizzolato M, Siebner HR, Dyrby TB. (2025). Axonal Structure-Function relationships across experimental modalities. Imaging Neuroscience 2025; doi: https://doi.org/10.1162/IMAG.a.1058