Thanks for the interest in our work entitled ‘The human phantom: Comprehensive ultrahigh resolution whole brain in vivo single subject dataset’.

Here, we present an extension to our previously published structural ultrahigh isotropic resolution T1-weighted magnetic resonance imaging (MRI) dataset, consisting of multiple additional high quality contrasts. Included are up to 150 μm Time-of-Flight (ToF) angiography, an updated 250 μm structural T1-weighted reconstruction, 330 μm quantitative susceptibility mapping (QSM), up to 450 μm structural T2-weighted imaging, 800 μm diffusion tensor imaging (DTI), one hour continuous resting state functional MRI (rs-fMRI) with an isotropic spatial resolution of 1.8 mm as well as more than 120 structural T1-weighted volumes collected over ten years with varying isotropic spatial resolution including corresponding proton density weighted acquisitions.

Data were acquired of one healthy right-handed Caucasian male subject (born 1982) with no known neurodegenerative or psychiatric disease. The first data were collected in 2009 and the latest in 2020. The subject gave written informed consent prior to each study and, retrospectively, to share all data publicly. The local ethics committee has approved each study. All data were acquired at the same 7 T MR scanner (7T Classic, Siemens Healthineers, Erlangen, Germany). From 2009 to 2011 data were acquired with a 1 Tx/24 Rx channel head coil (Invivo, Gainsville, FL, USA) and from 2012 onwards with a 1 Tx/32 Rx channel head coil (Nova Medical Inc, MA, USA). Many data were acquired with prospective motion correction (MT384i, Metria Innovation Inc., WI, USA). The DTI and rs-fMRI data were distortion corrected by using a point-spread function approach (https://dx.doi.org/10.1007/s10334-011-0275-6).

The repository contains unprocessed data as well as (pre-)processing results. The data were not acquired in a single study, but different studies with individual goals. This is a unique and very comprehensive collection comprising a “human phantom” dataset. Therefore, we compiled, processed, and structured the data, making them freely available to other researchers for further investigation. The repository is mostly structured according to BIDS. Whenever this was not possible, we tried to name the files as accurate as possible following BIDS regulations. In case you find something ambiguous or you identify an error, please get in contact with us.

In the root directory, you will find a folder named ‘sourcedata’, ‘derivatives’ as well as 'rawdata'. In rawdata, the scanner's raw data of the back-to-back scans can be found. In sourcedata, you will find all unprocessed NIfTI files, which were generated using ‘dcm2bids’ (v. 2.1.4) from the DICOM data of the MR scanner. In cases where this was not possible the according JSON file will be missing currently. However, if this has happened, we include an export of the scanning protocol in order to reproduce the acquisition.

The sourcedata ultrahigh resolution DTI data can be found in /soucedata/sub-yv98/ses-4284/, the QSM data in /sourcedata/sub-yv98/ses-4088/ as well as /sourcedata/sub-yv98/ses-4137/. the 250 µm ToF data in /sourcedata/sub-yv98/ses-3568/, the 150 µm ToF data in /sourcedata/sub-yv98/ses-3943/, and the rs-fMRI data in /sourcedata/sub-yv98/ses-5124/. The back-to-back scans can be found in /sourcedata/sub-yv98/ses-4496/. The eight repititions of the 250 µm MPRAGE data have been acquired in sessions 3512, 3555, 3589, 3637, and 3681.

In the folder derivatives, you will find all data created using the sourcedata. This includes the longitudinal data as well as ultrahigh resolution data. The individual results of processing the QSM, DTI, ToF, and rs-fMRI data can be found in their respective folders /derivatives/sub-yv98/QSM, /derivatives/sub-yv98/DTI, /derivatives/sub-yv98/ToF, and /derivatives/sub-yv98/rs-fMRI.

All ultrahigh resolution data have been registered to our previously published T1w ultrahigh resolution T1w MPRAGE with an isotropic resolution of 250 µm (https://datadryad.org/stash/dataset/doi:10.5061/dryad.38s74). The result of the registration can be found in /derivatives/sub-yv98/250um/registrations/. The registration has been conducted with ANTs using the included modified script "antsRegistrationSciData.sh" and the according transformation files can be found in /derivatives/sub-yv98/250um/registrations/transformations.

The longitudinal data has been quality check using MRIQC (/derivatives/sub-yv98/longitudinal_T1w/MRIQC) and biasfield correction using SPM12 (/derivatives/sub-yv98/longitudinal_T1w/biasfield) of all T1w volumes. Subsequently, all T1w volumes have been processed using the cross-sectional stream of FreeSurfer (v.6) with default parameters, which includes resampling to an isotropic resolution of 1 mm (/derivatives/sub-yv98/longitudinal_T1w/FreeSurfer).

An updated version of the 250 µm T1w MPRAGE is included in this repository. It is registered using a BSpline instead of a linear interpolator /derivatives/sub-yv98/250um/averages/. Therefore, the volume is much sharper, but also visually more noisy. To that end, the data has been denoised during reconstruction using in-house reconstruction pipeline (https://github.com/fluese/reconstructionPipeline). You can find the results of the offline reconstruction in /derivatives/sub-yv98/250um/reconstructions. This offline reconstructed dataset has been averaged, too (/derivatives/sub-yv98/250um/averages). The raw data of the 250 µm data in ISMRM raw data format can be found in the original publication (http://hiresmri.ovgu.de/).

The same offline reconstruction has been applied to the back-to-back scans, which can be found in /derivatives/sub-yv98/back-to-back/reconstructions/ as well as its averages (/derivatives/sub-yv98/back-to-back/averages).

All data in the dataset are shared under CC-0 license.

In case you have any questions, remarks, or just want to share your thoughts, please feel free to contact us.

Falk Luesebrink (falk dot luesebrink at med dot ovgu dot de)