Dataset from "Functional networks in the infant brain during sleep and wake states"

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Yates, T. S., Ellis, C. T., & Turk-Browne, N. B. (2023). Functional networks in the infant brain during sleep and wake states. Cerebral Cortex.

This directory contains raw and pre-processed resting state and movie watching data used for the analyses in the manuscript. To analyze this data, you should refer to the https://github.com/ntblab/infant_neuropipe/tree/RestingState/. In particular, https://github.com/ntblab/infant_neuropipe/tree/RestingState/scripts/RestingState/RestingState.ipynb utilizes these files to recreate the figures reported in the paper. For this purpose, the contents of this directory are expected to be in a folder called data/RestingState. This notebook can be adapted to explore other analyses, which in some cases will create new files.

Aeronaut is a 3-minute long segment of a short film entitled ''Soar'' created by Alyce Tzue (https://vimeo.com/148198462). The film was downloaded from YouTube in Fall 2017 and iMovie was used to trim the length. In the video, a girl is looking at airplane blueprints when a miniature boy crashes his flying machine onto her workbench. The pilot appears frightened at first, but the girl helps him fix the machine. After a few failed attempts, a blueprint flies into the girl's shoes, which they use to finally launch the flying machine into the air to join a flotilla of other ships drifting away. In the night sky, the pilot opens his suitcase, revealing a diamond star, and tosses it into the sky. The pilot then looks down at Earth and signals to the girl, who looks up as the night sky fills with stars. (Segments: 0:40 -- 2:30, 3:16 -- 4:26)

Mickey is a 2-minute and 20-second long segment of a popular cartoon (https://www.youtube.com/watch?v=hHCt2c_H0Ic). The video was downloaded from YouTube in Spring 2016. In this video, a surprise party is thrown where characters dance and play the piano while one character makes an exploding cake in the kitchen. (Segments: 0:06 -- 2:26)

In the functional imaging data provided, infants and adults watched these clips without audio presentation.

Resting state fMRI data was acquired differently in infants and adults: Infants were scanned during natural sleep, while adults viewed a fixation cross and were instructed to stay awake.

The scan sequences are as follows:

> MPRAGE: TR= 2300 ms, TE = 900 ms, flip angle = 9 degrees, iPAT = 2, matrix = 256 x 256, slices = 176, resolution = 1.00 mm isotropicPETRA: TR1 = 3.32 ms, TR2 = 2250 ms, TE = 0.07 ms, flip angle = 6 degrees, matrix = 320 x 320, slices = 320, resolution = 0.94 mm isotropic, radial slices = 30,000SPACE: TR = 3200 ms, TE = 563 ms, flip angle = 120 degrees, matrix = 192 x 192, slices = 176, resolution = 1 mm isotropicT2* gradient-echo EPI: TR = 2 s, TE = 30 ms, flip angle = 71 degrees, matrix = 64 x 64, slices = 34, resolution = 3 mm isotropic, interleaved slice acquisition

All files with the suffix '.nii.gz' or '.nii' can be opened using the freely-available fMRIB Software Library (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki) or open-source software FreeSurfer (https://surfer.nmr.mgh.harvard.edu/).

Description of the data and file structure

intersect_mask_standard.nii.gz: a brain mask file signaling which voxels are shared among all participants (value of 1) or are outside of the brain.

Adult_Aeronaut, Adult_Mickey, Adult_Rest, Infant_Aeronaut, Infant_Mickey, Infant_Sleep

Files in these folders contain raw and preprocessed infant or adult data.

Participant-specific files are named with the participant name at the start. The infant participant names are comprised of three parts: sXXXX describes the unique family ID, the _X that follows is the sibling ID (counting up from the first child to participate in the family) and the final _X is the session number. Hence: s0001_2_4 would be the 4th session for the 2nd sibling in family s0001. These infant participant IDs are consistent across datasets from the NTB Lab. Adult participant files are simply named based on their subject number and the study of acquisition (e.g., "mov", "mickey", "adult_ret", and "rest_movie"). Note that some "mov" participants came back for a second viewing --- these sessions are marked with "_2" at the end of the participant ID.

Run numbers indicate the nth run that was retained in that participant's session. If the number has a letter after it (e.g. functional03a) then that indicates it is a pseudorun and there is other data from this run that has been removed (because it pertained to another task, not reported here). All data within a run is continuous, no interleaved time points were removed.

> *_participants.csv: Summary table of the participant information, including: the participant ID, participant age (in years or months), participant sex (male or female), the functional run ID, the total number of TRs collected (num_TR), the proportion of TRs that were usable after motion exclusion (prop_TR_motion) and the average framewise displacement across the run (avg_FD). For infant movies, there are additional columns for the proportion of TRs that were usable after eye-tracking exclusion (prop_TR_eye), the proportion of frames that were coded the same between gaze coders (reliability; left blank if there was only one gaze coder), and the number of gaze coders (num_coders).

> anatomicals: Anatomical images used for alignment. Facial information has been stripped for anonymity. These were collected using the PETRA sequence (for infants) or the MPRAGE sequence (for adults) defined above. In some cases, more than one scan has been averaged to improve quality.

> connectivity_maps: Whole-brain functional connectivity matrices for each participant and run, used in the analysis notebook for main analyses. Default files use 3mm of motion threshold, while stricter motion threshold files are noted with *_fslmotion_0.2mm. Results are available for the Schaefer-100 parcellation atlas and the Scheinost-95 parcellation atlas.

> eye_confounds: Text files with 1s for TRs that should be excluded for eye closure. This folder is absent for infant sleep and all adult scans.

> motion_confounds: Text files with columns for motion parameters (three translational and three rotational --- if, however, these were highly correlated, only a subset are included) and TRs that should be excluded for excessive motion (with a value of 1 at the confound TR). Default files use 3mm of motion threshold, while stricter motion threshold files are noted with *_fslmotion_0.2mm.

> motion_metrics: Text files with framewise displacement values for each TR.

> preprocessed_native: Contains nifti files for preprocessed functional data. All functional images were linearly aligned to native anatomical space. Default files use 3mm of motion threshold, while stricter motion threshold files are noted with *_fslmotion_0.2mm.

> preprocessed_standard: Contains nifti files for preprocessed functional data during movie watching that have been aligned to standard MNI space nonlinearly with ANTs (subfolder nonlinear_alignment). Default files use 3mm of motion threshold, while stricter motion threshold files are noted with *_fslmotion_0.2mm.

> raw_nifti: Raw functional data for each run where movie task data was collected in these participants. If another task, not reported here, was completed in the same run then a pseudo-run was created in which the TRs corresponding to this task were sliced and separated.

> raw_timing: Timing information for the start of each block and event for each participant. For each file the first column is the onset of the event or block, the second column is the duration of event or block and the third column is the weight.

> > run_burn_in.txt: File with subject name, functional run, and number of TRs in the burn-in for that run (by default should be 3, but may differ)

> transformation_mats: The 4x4 affine transformation matrix (in .mat format) to align each functional in raw_nifti to the highres anatomical for that participant.

> transformation_ANTs: Contains ANTs folders for each participant. These were created by run_ANTs_highres2standard.sh and were used to create the nonlinear registration to infant standard and linear registration to adult MNI standard. Note that for adults, the infant_standard2standard.mat is an identity matrix, meaning that alignment to 'infant_standard' vs 'standard' is identical, and all references to 'infant_standard' actually refer to adult MNI space.
> > example_func2highres.nii.gz: functional image of the centroid TR that minimizes the Euclidian distance between TRs aligned to highres anatomical space*example_func2infant_standard.nii.gz: functional image of the centroid TR that minimizes the Euclidian distance between TRs aligned to infant standard spaceexample_func2standard.nii.gz: functional image of the centroid TR that minimizes the Euclidian distance between TRs aligned to adult MNI standard spaceexample_func.nii.gz: functional image of the centroid TR in its native 3mm spacefs_alignment.mat: transformation matrix that aligns fs_vol.nii.gz to highres_brain.nii.gz (6 degrees of freedom)
> > **fs_brain.nii.gz: freesurfer-outputted highres anatomical image rotated and masked to only show brain voxelsfs_vol.nii.gz: freesurfer-outputted highres anatomical image in 1mm spacehighres2infant_standard_0GenericAffine.mat: transformation matrix used to move from highres to infant standard spacehighres2infant_standard_1InverseWarp.nii.gz: warp file used by ANTs to move from infant standard space to highreshighres2infant_standard_1Warp_3mm.nii.gz: warp file used by ANTs to move from high resolution to infant standard space (while maintaining 3mm functional space)highres2infant_standard_1Warp.nii.gz: warp file used by ANTs to move from high resolution to infant standard spacehighres2infant_standard_InverseWarped.nii.gz: infant standard image aligned to highres space via ANTshighres2infant_standard_Warped.nii.gz: highres anatomical image aligned to infant standard space via ANTshighres2standard.nii.gz: highres anatomical image aligned to adult MNI standard spaceinfant_standard2standard.mat: linear transformation matrix between infant standard and adult MNI standard spacehighres_brain.nii.gz: highres anatomical image masked to only show brain voxelsinfant_standard.nii.gz: infant standard image, determined based on the child's agemask.nii.gz*: mask to facilitate anatomical alignment to standard, manually edited from freesurfer output

circos_data

Average contributions to similarity for whole-brain brain functional connectivity matrices (or difference matrices) that are used in the notebook for creating Circos plots. These are saved as numpy files to be opened using Python. Please see notebook for more details on how these files are created and used.

plots

Empty folder to contain figures created from the notebook.

Sharing/Access information

Some of this data was previously reported in: Yates, T. S., Skalaban, L. J., Ellis, C. T., Bracher, A. J., Baldassano, C., & Turk-Browne, N. B. (2022). Neural event segmentation of continuous experience in human infants. Proceedings of the National Academy of Sciences, 119 (43), e2200257119.

Raw and preprocessed data from this previous paper can be found on DataDryad: https://datadryad.org/stash/dataset/doi:10.5061/dryad.vhhmgqnx1

Code/Software

The scripts in the infant_neuropipe repository can be used to run the analyses reported in the paper. The RestingState.ipynb notebook can regenerate the figures. Scripts in that directory can rerun the analyses, refer to the notebook and analysis README for more direction. Questions about the data or analyses can be directed to Tristan Yates, tristan.yates@yale.edu