Automated release for ds004884_3

An open relaxation-diffusion MRI dataset in neurosurgical studies

The MRI data was collected from 18 patients (including glioma, meningioma, diffuse large B-cell, multiple sclerosis, cortical cerebral infarction, and brain abscess) and two healthy individuals (11 females and 9 males; age range: 28.0 - 70.0 years; median age: 51.0 years; IQR: 21.5 years). The rdMRI data is acquired on a 3T Philips MRI scanner with 7 TEs (two healthy individuals has only 5 TEs, sub-05 and sub-15). All participants provided written informed consent before participation and signed informed consent regarding publishing their data. The Research Ethics Committee, Faculty of Medicine in Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, China approved the study protocols.

Contact information:

• Name: Ye Wu
• Email: dr.yewu@outlook.com

Of all subjects the following data were acquired:

• T1-weighted three-dimensional (3D) turbo field-echo (TFE) anatomical scan (anat)
• multi-echo multi-shell HARDI diffusion-weighted MRI (dwi, acq=PA)
  • ses-01: TE=75ms, Delta=35.9ms, delta=19.9ms
  • ses-02: TE=85ms, Delta=40.9ms, delta=24.9ms
  • ses-03: TE=95ms, Delta=45.9ms, delta=29.9ms
  • ses-04: TE=105ms, Delta=50.9ms, delta=34.9ms
  • ses-05: TE=115ms, Delta=55.9ms, delta=39.9ms
  • ses-06: TE=125ms, Delta=60.9ms, delta=44.9ms
  • ses-07: TE=135ms, Delta=65.9ms, delta=49.9ms
• demographic information

The "derivatives" folder contains:

• dwipreproc, preprocessed dwi dataset
• anatpreproc, preprocessed anat dataset, and tissue segmentation obtained with the SynthSeg toolbox described here https://doi.org/10.1016/j.media.2023.102789 and https://doi.org/10.1073/pnas.2216399120.
• freesurfer, cortical parcellation generated by Freesurfer v7.3.2
• dwiqc, quality assessment of dwi dataset, implemented with https://dsi-studio.labsolver.org/ and https://github.com/pnlbwh/SlicerDiffusionQC.
• anatqc, quality assessment of anat dataset, implemented with https://github.com/pnlbwh/structuralQC
• pathlogy, tumor pathology images

https://openneuro.org/datasets/ds004910

https://openneuro.org/datasets/ds004884

https://openneuro.org/datasets/ds004498

https://openneuro.org/datasets/ds003599

2020-11-10

CITATION:
Snider SB, Bodien YG, Frau-Pascual A, Bianciardi M, Foulkes AS, Edlow BL.
Ascending arousal network connectivity during recovery from traumatic
coma. NeuroImage:Clinical. 2020; in press. PMCID pending.

EXPERIMENT
Our goal was to identify the connections with the ascending arousal network with 1) the largest change during recovery of consciousness after a TBI and 2) had the largest connectivity differences between subjects with or without a chronic disorder of consciousness.

We pulled from a dataset of N = 18 subjects with acute severe TBI and coma(GCS <= 6, no eye opening for 24 hours, abnormal CT scan). 2 subjects (sub-TCRp014, sub-TCRp016) died during the acute hospitalization and were excluded from analyses in the manuscript above. All others recovered consciousness. 9 subjects had follow-up imaging >= 5 months after the initial hospitalization, while 7 subjects did not.

For comparison, we included N = 16 age,sex-matched control subjects and a convenience sample of N = 6 subjects with a chronic disorder of consciousness (DoC) >= 5 months following their TBI.

DATA
Data included herein at this time only include the HARDI volumes, skull-stripped (bet2) for deidentification.

Acquired on 3T Skyra (Siemens) using 32-channel head coil. HARDI scan params: 2mm isotropic resolution, 60 diffusion encoding directions, 10 b0 volumes, b=2000 sec/mm2.

SUBJECT GROUPINGS
TBI recovery patients, longitudinal imaging(N = 9):
sub-TCRp001 ses-early ses-late
sub-TCRp003 ses-early ses-late
sub-TCRp005 ses-early ses-late
sub-TCRp006 ses-early ses-late
sub-TCRp008 ses-early ses-late
sub-TCRp013 ses-early ses-late
sub-TCRp017 ses-early ses-late
sub-TCRp018 ses-early ses-late
sub-TCRp023 ses-early ses-late

TBI patients, acute imaging only(N = 9)
sub-TCRp007 ses-early
sub-TCRp009 ses-early
sub-TCRp010 ses-early
sub-TCRp011 ses-early
sub-TCRp012 ses-early
sub-TCRp014 ses-early
sub-TCRp015 ses-early
sub-TCRp016 ses-early
sub-TCRp022 ses-early

Chronic DOC (N = 6):
sub-TCRp002 ses-late
sub-TCRp019 ses-late
sub-TCRp020 ses-late
sub-TCRp021 ses-late
sub-TCRp024 ses-late
sub-TCRp025 ses-late

Age/Sex-matched healthy controls (N = 16):
sub-TCRc* ses-1

https://openneuro.org/datasets/ds003367

The SUDMEX_CONN dataset is the result of a case-control study of cocaine use disorder patients. The study was done at the National Institute of Psychiatry in Mexico City by PIs Dr. Eduardo A. Garza-Villarreal and Jorge J. Gonzalez Olvera.

The MRI sequences were: 1) T1-weighted, 2) rsfMRI 10 min, 3) HARDI-DWI multishell.

Full clinical data will be uploaded to Zenodo soon. This is the first official release.
https://openneuro.org/datasets/ds003346

The SUDMEX_TMS dataset is the result of a longitudinal clinical trial of cocaine use disorder patients that were treated with rTMS at 5-Hz on the left dorsolateral prefrontal cortex (lDLPFC) for a 2 week double-blind acute phase and an open-label maintenance phase that included clinical, cognitive and MRI data acquisition. The design was a double-blind placebo-controlled randomized controlled trial with parallel groups (acute phase). The study was done at the National Institute of Psychiatry in Mexico City by PIs Dr. Eduardo A. Garza-Villarreal and Dr. Ruth Alcala-Lozano.

Each patient had more than one clinical and MRI session or time point from baseline (T0), 2 weeks (T1), 3 months (T2), 6 months (T3) and some patients had 12 months (T4). The T14 time point was only for patients in the Sham group who decided to continue the clinical trial with open-label rTMS. The T14 refers to 2 weeks after T1 (4 weeks after T0).

The MRI sequences were: 1) T1-weighted, 2) rsfMRI 10 min, 3) HARDI-DWI multishell (next release).

Full clinical data will be uploaded to Zenodo soon. This is the first official release.
https://openneuro.org/datasets/ds003037