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ds006688_2
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ds006688_1
Automated release for ds006688_1
Penn LEAD: Penn Longitudinal Executive functioning in Adolescent Development
Penn LEAD: Penn Longitudinal Executive functioning in Adolescent Development
Penn LEAD is a longitudinal dataset consisting of clinical, cognitive, and multimodal neuroimaging data from 132 adolescents, designed to investigate transdiagnostic executive function during development.
Note that in some cases, there may be more runs than expected or noted in dataset contents below if a run was repeated. If a run was repeated, there might be an extra run in the dataset. Additionally, in cases where the data from one of the runs was poor quality, there might be a second and third run but no first run.
Any variant to the metadata that might differ from what is described below will be flagged in the file name for that scan in the acquisition entity (i.e., sub-\*_ses-\*_acq-VARIANT{variant_description}_run-\*_\*.*)
Dataset contents
Structural MRI
Each participant has one T1-weighted normalized scan (176 slices, TR = 2500 ms, TE = 2.9 ms), one T2-weighted (not normalized) scan (176 slices, TR = 3200 ms, TE = 565 ms), and one T2-weighted normalized scan, all with the AP phase encoding direction. T1 scans are refaced and T2 scans are defaced. The processed sMRI data derivatives can be found here.
Functional MRI
Each participant has two resting-state fMRI runs (522 volumes and 383 volumes, TR = 800 ms, TE = 30 ms, 60 slices) and one n-back task fMRI run with fractal images (522 volumes, TR = 800 ms, TE = 30 ms, 60 slices). The processed fMRI data derivatives can be found here and here.
Note that for one subject, they had to re-run the resting-state fMRI, since in the first run, a movie was accidentally playing in the first run. Hence, the task entity was renamed to task-restfilm.
Diffusion MRI
One 103-volume multi-shell (MB = 3), single spin-echo DWI run was acquired for all participants using a monopolar sampling scheme (TR = 4200 ms, TE = 89 ms, voxel size = 1.7 mm isotropic). The processed DWI data derivatives can be found here and here.
Perfusion MRI
One background-suppressed, unbalanced, 3D stack of spirals PCASL scan was acquired for all participants (labeling duration = 1500 ms, TR = 4298 ms, TE = 10 ms). The processed ASL data derivatives can be found here.
A reference scan was also acquired to assist in ASL calibration, consisting of an M0 scan that is retained in the perfusion folder with the m0scan suffix.
MEGRE
We acquired a multi-echo gradient-echo sequence with four echos, for use in quantitative susceptibility mapping (QSM), at 1.5 mm isotropic resolution (TR = 35 ms, voxel size = 1.5 * 1.5 * 1.5 mm).
Note that we did not curate or preprocess the MEGRE data, but raw data can be found in the dataset.
Field maps
For distortion correction, pairs of field maps with opposite phase-encoding polarity (anterior to
posterior and posterior to
anterior) were acquired for both diffusion-weighted and fMRI scans.
Phenotypic Data
Clinical diagnostic data can be found in the participants.tsv file.
Cognitive Data
Participants completed a number of cognitive tasks from the Penn CNB. These included:
- Penn Abstraction, Inhibition and Working Memory Task
- Penn Face Memory Test
- Children's Penn Word Memory Test
- Short Computerized Finger-Tapping Task
- Penn Emotion Recognition Task for Children
- Digit Symbol Test
- Short Letter N-Back (2 back)
- Measured Emotion Differentiation Test
- Motor Praxis Test
- Penn Conditional Exclusion Task for Children
- Short Penn Continuous Performance Test - Number and Letter Version
- Penn Matrix Reasoning Test
- Variable Short Penn Line Orientation Test
- Children's Verbal Reasoning Test
- Short Visual Object Learning Test
- Trailmaking A
- Trailmaking B
- Effort Discounting Task
- Delayed Discounting Task
- Risk Discounting Task
- Age Differentiation Test
The following subjects/sessions are missing cognitive data:
- sub-21161, ses-1
- sub-22510, ses-2
- sub-22617, ses-2
- sub-22618, ses-2
- sub-23582, ses-1
- sub-20812, ses-2 had a session 1 that was started, but incomplete, and a session 2 that began a couple of days later. As such, we only have CNB data from ses-1, and ses-3, but ses-2 did not have a separate CNB administered.
Other data
The acquisition date and time for each session was rounded to the 15th of the month and the nearest hour, and stored in the *_sessions.tsv files.
Additional notes
Note that sub-20812 has two sessions (ses-1 and ses-2) that are only a few days apart. Ses-1 contains incomplete data and thus the scans were repeated a few days later for ses-2.
The impact of multiband and in-plane acceleration on white matter microstructure and connectivity study
MIND: Multilingual Imaging Neuro Dataset
A fMRI neuroimaging dataset of word reading with semantic and phonological localizers in children and adolescents
Connectome 2.0 Diffusion MRI (in vivo)
Longitudinal-Trajectories-Early-Brain-Development-Language
This repository contains one of two datasets used in the following study:
Turesky TK, Escalante ES, Loh M, Gaab N. Longitudinal trajectories of brain development from infancy to school age and their relationship to literacy development, https://doi.org/10.1101/2024.06.29.601366.
For the other dataset, please see https://osf.io/axz5r/.
All participants included in this repository had MR images from at least two timepoints that passed the QC standards for the manuscript referenced above. Any MR images for these participants from additional timepoints were also included regardless of whether they passed the QC standards.
Please note that session numbers correspond to the following developmental timepoints:
ses-01 = infant
ses-02 = toddler
ses-03 = pre-reading
ses-04 = beginning reading
ses-05 = emergent reading
FreeSurfer's mri_deface was used to deface all T1w images, except for the following partipants, for whom we used mideface:
Images where mri_deface did not sufficiently distort the face:
sub-04/ses-03
sub-29/ses-04
sub-34/ses-02
sub-52/ses-04
sub-55/ses-01
sub-65/ses-04
sub-70/ses-05
sub-72/ses-03
Images where mri_deface cut into brain tissue:
sub-12/ses-03
sub-12/ses-04
sub-15/ses-05
sub-57/ses-05
sub-62/ses-05
sub-79/ses-04
Data dictionary for measures:
participant_id - participant IDs
timepoint - INF=infant, TOD=toddler, PRE=pre-reading, BEG=beginning reading, REA=emergent reading
session - timepoint number
age - age in months
Sex - biological sex (0=male, 1=female)
MEd - maternal education
HLE - home literacy composite (z-normalized)
FHD - family history of dyslexia (0=none, 1=first degree relative)
pre_word_access_raw - PRE WJIV word access subtest raw
pre_word_fluency_raw - PRE WJIV word fluency subtest raw
pre_substitution_raw - PRE WJIV substitution subtest raw
pre_wjiv_oralcomp_raw - PRE WJIV oral comprehension subtest raw
pre_wjiv_pvocab_raw - PRE WJIV picture vocabulary subtest raw
pre_wjiv_phonproc_standard - PRE timepoint WJIV phonological processing standardized composite
pre_wjiv_orallang_standard - PRE timepoint WJIV oral language standardized composite
kbit2_raw - KBIT reasing subtest raw score
kbit2_standard - KBIT reasing subtest standard score
beg_wrmt3_wrd_id_raw - BEG timepoint WRMT word id raw score
beg_wrmt3_wrdatt_raw - BEG timepoint WRMT word attack raw score
beg_wrmt3_wrd_id_stnd - BEG timepoint WRMT word id standard score
beg_wrmt3_wrdatt_stnd - BEG timepoint WRMT word attack standard score
pre_beh_age - age at PRE timepoint
beg_beh_age - age at BEG timepoint
euler - Euler number rating for T1 images, average of hemispheres (FreeSurfer metric)
qc_s - visual ratings of FreeSurfer segmentations (0=poor, 1=regional-localized errors, 2=good)
qc_ARC_L - visual ratings of py(Baby)AFQ tracts (0=poor, 1=sparser than usual, 2=good)
qc_ARC_R - visual ratings of py(Baby)AFQ tracts (0=poor, 1=sparser than usual, 2=good)
qc_ILF_L - visual ratings of py(Baby)AFQ tracts (0=poor, 1=sparser than usual, 2=good)
qc_ILF_R - visual ratings of py(Baby)AFQ tracts (0=poor, 1=sparser than usual, 2=good)
qc_SLF_L - visual ratings of py(Baby)AFQ tracts (0=poor, 1=sparser than usual, 2=good)
qc_SLF_R - visual ratings of py(Baby)AFQ tracts (0=poor, 1=sparser than usual, 2=good)
Keys for remaining variables may be found in Table S1 of the following citation: Yu X, et al. (2021) Functional Connectivity in Infancy and Toddlerhood Predicts Long-Term Language and Preliteracy Outcomes. Cerebral Cortex 32, 725–736.
For corresponding code, please see https://github.com/TeddyTuresky/Longitudinal-Trajectories-Early-Brain-Development-Language/tree/main.
Psilocybin Precision Functional Mapping (data from Psilocybin desynchronizes the human brain)
GeneratedBy : niix2bids==v2.5.0
BIDSVersion : v1.6.0
Psilocybin's acute and persistent effects
Here, we present a randomized cross-over study using precision functional mapping to characterize acute and persistent effects of psilocybin (PSIL) or methylphenidate (MTP) on brain networks. Seven healthy volunteers (mean age 34.1 years, SD=9.8; n=3 females, n=6 Caucasians) underwent 1) extensive baseline imaging, 2) imaging beginning 60-90 minutes after drug exposure, and 3) longitudinal imaging for up to two weeks after drug exposure. Four individuals also participated in an open-label PSIL replication protocol over 6 months later. This dataset includes rsfMRI (using advanced high-resolution multi-echo fMRI), task fMRI, structural, and diffusion basis spectral imaging as well as assessments of subjective experience.
MRI Data Description
-Siemens Prisma scanner
-structural MRI (T1- and T2-weighted images), 0.9 mm isotropic resolution
-resting state fMRI scans (513 frames, 15 minutes each)
-task fMRI scans (233 frames, 6 minutes and 50 seconds each)
Resting state and task scans used an echoplanar imaging sequence with multi-echo (five TEs: 14.20 ms, 38.93 ms, 63.66 ms, 88.39 ms, 113.12 ms), TR 1761 ms, flip angle = 68 degrees, and in-plane acceleration (IPAT/grappa) = 2 [34, 35]. This sequence acquired 72 axial slices (144 mm coverage).
-Nordic Denoising compatible: fMRI scans included 3 noise scans at the end of each run, and mag and phase images are included.
#Participant information
- Total participants, N = 7
- Total participants who completed replication, N=4 (P1, P3, P4, P5)
REST SCANS
P1 P2 P3 P4 P5 P6 P7 P1R P3R P4R P5R
NonDrug 33 36 26 27 28 21 26 11 6 7 7
PSIL 2 2 1 1 4 2 5 4 3 2 3
MTP 2 2 2 3 4 3 3 0 0 0 0
TASK SCANS
NonDrug 12 14 11 5 4 6 12 2 0 2 4
PSIL 2 2 2 2 0 0 2 2 0 2 2
MTP 2 2 2 2 0 2 2 0 0 0 0
ORDER
SubID Drug1 Drug2
P1 MTP PSIL
P2 PSIL MTP
P3 MTP PSIL
P4 MTP PSIL
P5 PSIL MTP
P6 MTP PSIL
P7 PSIL MTP
P1R PSIL
P3R PSIL
P4R PSIL
P5R PSIL
##Notes from MRI sessions
PPFM_session_notes.xlsx
session_data.csv
- Any rest scans that were ended early for any reason (e.g. P6 ses-5 REST3, P4R ses-2 REST3,) will not have the 3 noise images at the end. We copied noise frames from neighboring a rest scan so this did not interfere with NORDIC denoising.
Phenotypic Data Description
PPFM_MEQ_DATA.xlsx
Inclusion/Exclusion Criteria
Please see https://clinicaltrials.gov/study/NCT00088699 for a detailed list, also included below.
#Inclusion Criteria:
-Healthy men and woman between 18 and 45 years of age;
-Have used a psychedelic substance within the previous 5 years but not within the last 6 months;
-No active psychiatric conditions requiring treatment with psychotropic medications (may be included if psychiatric condition is stable and participant is willing to discontinue medication for 1 month prior to participation with permission from their treating provider);
-Able to provide informed consent.
Exclusion Criteria:
-Presence of medical conditions that may confound results of imaging study or that are contraindications to psilocybin exposure (e.g. neurological, renal, hypertension, metabolic or cardiovascular disease or pregnancy);
-No prior exposure to classic psychedelics (psilocybin, LSD, ayahuasca, mescaline);
-Presence of psychiatric conditions that may confound interpretation of results or that are contraindications to psilocybin exposure (e.g. major mood disorder, current substance use disorder, personal or immediate family history (parents, siblings) of any schizophrenia spectrum disorders);
-Use of psychotropic medication during the study;
-Presence of contraindications to MRI scanning (implantable devices, bone hardware, IUD).
-Prior adverse reactions to psychedelics, based on the Challenging Experiences -Questionnaire administered during initial screening
NON_BIDS
NON_BIDS folder contains processed ciftis
https://openneuro.org/datasets/ds006072
Sustained Attention Task (gradCPT) Dataset using simultaneous EEG-fMRI and DTI
This dataset includes simultaneous recordings of electroencephalography (EEG), functional magnetic resonance imaging (fMRI), and diffusion-weighted imaging (DWI) from 28 participants aged 19 to 42 years. The fMRI and DWI data were acquired using a 3T MRI scanner (Siemens Magnetom Prisma), and the EEG was recorded using 64 channels (Brain Product BrainCap MR with Multirodes).
The following tasks were performed: resting state (eyes open and closed), checkerboard (15Hz), gradCPT, and imagery task. Raw files can be found in the subfolders, while preprocessed files are available in the derivatives folder. For more detailed information about the file structure, please refer to the readme files.
https://openneuro.org/datasets/ds006040