DOI: 10.5061/dryad.119f80q
title: Data from: 7 Tesla MRI of the ex vivo human brain at 100 micron resolution

description: We present an ultra-high resolution MRI dataset of an ex vivo human brain
 specimen. The brain specimen was donated by a 58-year-old woman who had no
 history of neurological disease and died of non-neurological causes. After
 fixation in 10% formalin, the specimen was imaged on a 7 Tesla MRI scanner
 at 100 µm isotropic resolution using a custom-built 31-channel receive
 array coil. Single-echo multi-flip Fast Low-Angle SHot (FLASH) data were
 acquired over 100 hours of scan time (25 hours per flip angle), allowing
 derivation of synthesized FLASH volumes. This dataset provides an
 unprecedented view of the three-dimensional neuroanatomy of the human
 brain. To optimize the utility of this resource, we warped the dataset
 into standard stereotactic space. We now distribute the dataset in both
 native space and stereotactic space to the academic community via multiple
 platforms. We envision that this dataset will have a broad range of
 investigational, educational, and clinical applications that will advance
 understanding of human brain anatomy in health and disease.
description: Synthesized FLASH25 100
 Micron MRI The synthesized FLASH25
 volume from the 100 Micron MRI scan is the volume that provides the best
 contrast for visualization of human neuroanatomy. We recommend this volume
 for users who are interested in human brain anatomy. A detailed
 description of the synthesized FLASH25 volume is provided in the
 manuscript associated with this dataset, in the "MRI data
 processing" subsection of the Methods. In short, the synthesized
 FLASH25 volume is recomputed from all acquired volumes associated with
 this 100 micron MRI scan. The code used to generate the synthesized
 FLASH25 volume from the acquired volumes can be found at
 https://surfer.nmr.mgh.harvard.edu/fswiki and is described in detail in
 the README file associated with the corresponding OpenNeuro data release.
 For users who would like to visualize the images before downloading this
 file, we refer you to an online viewer at which the synthesized FLASH25
 volume can be visualized: https://histopath.nmr.mgh.harvard.edu/. The
 synthesized FLASH25 volume can also be visualized on our YouTube channel:
 https://www.youtube.com/playlist?list=PLlL7CEMX5bxzl1TqkJRK3pMV4Ax6By4bN. Synthesized_FLASH25_100um.nii.gz Synthesized FLASH25 100 Micron MRI – Axial Images This zip file includes all axial images of the synthesized FLASH25 volume from the 100 micron MRI dataset. For users who would like to visualize the images before downloading this file, we refer you to an online viewer at which the synthesized FLASH25 volume can be visualized: https://histopath.nmr.mgh.harvard.edu/. The synthesized FLASH25 volume can also be visualized on our YouTube channel: https://www.youtube.com/playlist?list=PLlL7CEMX5bxzl1TqkJRK3pMV4Ax6By4bN. Synthesized_FLASH25_100um_TIFF_Axial_Images.zip Synthesized FLASH25 100 Micron MRI – Coronal Images This zip file includes all coronal images of the synthesized FLASH25 volume from the 100 micron MRI dataset. For users who would like to visualize the images before downloading this file, we refer you to an online viewer at which the synthesized FLASH25 volume can be visualized: https://histopath.nmr.mgh.harvard.edu/. The synthesized FLASH25 volume can also be visualized on our YouTube channel: https://www.youtube.com/playlist?list=PLlL7CEMX5bxzl1TqkJRK3pMV4Ax6By4bN. Synthesized_FLASH25_100um_TIFF_Coronal_Images.zip Synthesized FLASH25 100 Micron MRI – Sagittal Images This zip file includes all sagittal images of the synthesized FLASH25 volume from the 100 micron MRI dataset. For users who would like to visualize the images before downloading this file, we refer you to an online viewer at which the synthesized FLASH25 volume can be visualized: https://histopath.nmr.mgh.harvard.edu/. The synthesized FLASH25 volume can also be visualized on our YouTube channel: https://www.youtube.com/playlist?list=PLlL7CEMX5bxzl1TqkJRK3pMV4Ax6By4bN. Synthesized_FLASH25_100um_TIFF_Sagittal_Images.zip Synthesized FLASH25 100 Micron MRI – Downsampled to 200 Micron For users who prefer to download a version of the synthesized FLASH25 volume that has a smaller file size, we created this downsampled volume at 200 micron spatial resolution. Synthesized_FLASH25_downsampled_200um.nii.gz Synthesized FLASH25 100 Micron MRI – Downsampled to 500 Micron For users who prefer to download a version of the synthesized FLASH25 volume that has a smaller file size, we created this downsampled volume at 500 micron spatial resolution. Synthesized_FLASH25_downsampled_500um.nii.gz Synthesized FLASH25 100 Micron MRI in MNI Space – Version 2 For users who would like to visualize, analyze and/or segment the 100 micron MRI dataset in MNI space, we coregistered the synthesized FLASH25 volume to the MNI ICBM 2009b NLIN ASYM template. This template constitutes the newest version of the “MNI space” and is considered a high-resolution version of MNI space because it is available at 0.5 mm isotropic resolution. Compared to version 1 (released on June 4, 2019), this new version 2 includes a more accurate coregistration of the cerebral cortex. The coregistration was performed using the Lead-DBS v2.0 software platform. Lead-DBS is a MATLAB-based, version-controlled software package whose code is available at GitHub (www.github.com/netstim/leaddbs). A detailed description of the synthesized FLASH25 volume in MNI space is provided in the manuscript associated with this dataset, in the "MRI data processing" and "Coregistration of the dataset to standard stereotactic space" subsections of the Methods. Synthesized_FLASH25_in_MNI_v2_100um.nii.gz Synthesized FLASH25 100 Micron MRI in MNI Space – Downsampled to 200 Micron For users who prefer to download a version of the MNI-coregistered, synthesized FLASH25 volume that has a smaller file size, we created this downsampled volume at 200 micron spatial resolution. Synthesized_FLASH25_in_MNI_v2_200um.nii.gz Synthesized FLASH25 100 Micron MRI in MNI Space – Downsampled to 500 Micron For users who prefer to download a version of the MNI-coregistered, synthesized FLASH25 volume that has a smaller file size, we created this downsampled volume at 500 micron spatial resolution. Synthesized_FLASH25_in_MNI_v2_500um.nii.gz Acquired FA25 100 Micron MRI The acquired FA25 volume from the 100 Micron MRI scan is the volume that best demonstrates the exquisite neuroanatomic resolution provided by acquisition of a single flip (FA25˚). We recommend this volume for users who are interested in investigating the acquired data prior to recomputing the synthesized volumes (e.g. the synthesized FLASH25 volume). A detailed description of the FA25 acquisition is provided in the manuscript associated with this dataset, in the "MRI data reconstruction" subsection of the Methods. Acquired_FA25_100um.nii.gz Acquired FA25 100 Micron MRI – Downsampled to 200 Micron For users who prefer to download a version of the acquired FA25 volume that has a smaller file size, we created this downsampled volume at 200 micron spatial resolution. Acquired_FA25_downsampled_200um.nii.gz Acquired FA25 100 Micron MRI – Downsampled to 500 Micron For users who prefer to download a version of the acquired FA25 volume that has a smaller file size, we created this downsampled volume at 500 micron spatial resolution. Acquired_FA25_downsampled_500um.nii.gz 100 Micron MRI Scan Protocol This protocol provides comprehensive details of all MRI sequence parameters that were used to perform the 100 micron MRI scan. 100_Micron_MRI_Scan_Protocol.pdf Dryad/OpenNeuro File Index This index provides a list of all files released via Dryad and OpenNeuro, with a key explaining how the file names on each respective site relate to one another. The reason that the file naming is not identical on the Dryad Digital Repository and OpenNeuro is that the OpenNeuro directory structure and naming convention are designed to be compliant with BIDS (version 1.1.1; https://bids.neuroimaging.io/bids_spec.pdf). Another difference between the Dryad Digital Repository and OpenNeuro data releases is that the OpenNeuro release includes additional source data files and a first-pass synthesized FLASH25 parameter map. For user convenience, in this Dryad Digital Repository release we have consolidated the data and removed the subject ID (“EXC004”) from the file names. We also aimed to enhance the usability of the files released here by reorienting all volumes to standard radiologic orientation, and by cropping all extraneous space surrounding the brain. Dryad_OpenNeuro_File_Index.pdf VIDEO 1 – 100 MICRON MRI ACQUIRED FA25 AXIAL This video shows all axial images from the acquired FA25 volume. VIDEO_1_100_MICRON_MRI_ACQUIRED_FA25_AXIAL.mp4 VIDEO 2 – 100 MICRON MRI ACQUIRED FA25 CORONAL This video shows all coronal images from the acquired FA25 volume. VIDEO_2_100_MICRON_MRI_ACQUIRED_FA25_CORONAL.mp4 VIDEO 3 – 100 MICRON MRI ACQUIRED FA25 SAGITTAL This video shows all sagittal images from the acquired FA25 volume. VIDEO_3_100_MICRON_MRI_ACQUIRED_FA25_SAGITTAL.mp4 VIDEO 4 – 100 MICRON MRI SYNTHESIZED FLASH25 AXIAL This video shows all axial images from the synthesized FLASH25 volume. The video can also be viewed on our YouTube channel: https://www.youtube.com/playlist?list=PLlL7CEMX5bxzl1TqkJRK3pMV4Ax6By4bN. VIDEO_4_100_MICRON_MRI_SYNTHESIZED_FLASH25_AXIAL.mp4 VIDEO 5 – 100 MICRON MRI SYNTHESIZED FLASH25 CORONAL This video shows all coronal images from the synthesized FLASH25 volume. The video can also be viewed on our YouTube channel: https://www.youtube.com/playlist?list=PLlL7CEMX5bxzl1TqkJRK3pMV4Ax6By4bN. VIDEO_5_100_MICRON_MRI_SYNTHESIZED_FLASH25_CORONAL.mp4 VIDEO 6 – 100 MICRON MRI SYNTHESIZED FLASH25 SAGITTAL This video shows all sagittal images from the synthesized FLASH25 volume. The video can also be viewed on our YouTube channel: https://www.youtube.com/playlist?list=PLlL7CEMX5bxzl1TqkJRK3pMV4Ax6By4bN. VIDEO_6_100_MICRON_MRI_SYNTHESIZED_FLASH25_SAGITTAL.mp4 VIDEO 7 – 100 MICRON MRI MOVIE This video shows all axial, coronal, and sagittal images from the synthesized FLASH25 volume. The video also provides a visual and descriptive summary of the methods that we used to create the 100 micron MRI scan. VIDEO_7_100_MICRON_MRI_MOVIE.mp4