CONP Portal | Dataset


Keywords: Structural MRI
High Resolution Magnetic Resonance Imaging of Mouse Model related to Autism
Creators: Ontario Brain Institute, Mouse Imaging Centre
Contact: Jacob Ellegood, Research Associate, jacob.ellegood@sickkids.ca
Licenses: Refer to Brain-CODE Governance Policy
Version: 1.0
Modalities: MRI
Formats: MINC CSV
Size: 208.9 GB
No of Files: 4299
No of Subjects: 839
Project Landing Page: https://www.braincode.ca/
Metadata file: DATS.json
Acknowledges: Ontario Brain Institute, Province of Ontario Neurodevelopmental Disorders, Government of Ontario
Spatial Coverage: Toronto
Other Dates: Release Date: 2018-02-01 -- Start Date: 2012-02-01 -- End Date: 2017-02-01
Description:
This dataset includes 31 mouse models representing 23 genotypes from their ongoing study of 90+ mouse strains

Dataset README information

README.md

High Resolution Magnetic Resonance Imaging of Mouse Model related to Autism

Overview

Drs. Jason Lerch, Jacob Ellegood, Mark Henkelman and their team at the Mouse Imaging Centre (MICe) at the Hospital for Sick Children have pioneered high throughput mouse brain Magnetic Resonance Imaging (MRI) to better understand how autism affects the brain.
In collaboration with multiple international and national labs, the team is using MRI to phenotype multiple mouse strains with genetic mutations that are known to be associated with autism.
These images capture the complex heterogeneity inherent in the autism spectrum and also identify key brain areas that are commonly involved across these mouse models.
The MRI images provide whole brain coverage, and with advanced image processing and statistics, allow the determination of alterations in brain structure or microstructure to a resolution of 40-80 microns.

This open data release includes 31 mouse models representing 23 genotypes from their ongoing study of 90+ mouse strains, which will continue to be shared in future releases.

This project was funded by the Ontario Brain Institute’s POND Program, with support from Brain Canada and CIHR.

Access

The dataset could be requested via authorized access on https://www.braincode.ca/.
To request data set on Brain-CODE, sign-up by clicking “Register”.
Registered portal users have access to interactive dashboards for data exploration and data download.

Download Using DataLad

CircleCI status

The following instructions require a basic understanding of UNIX/LINUX command lines. A subset of open datasets on the Portal are also available through a browser-based download button. The instructions below regard dataset download with the use of DataLad. To install DataLad on your system, please refer to the install section of the DataLad Handbook .

Note: For maximum compatibility with conp-dataset, the CONP recommends versions 3.12+ of Python, 10.20241202+ of git-annex, and 1.1.4+ of datalad.

1) Initiate the CONP dataset

Run the following command in the directory where you want the CONP dataset (conp-dataset) to be installed:

2) Install the braincode_Mouse_Image dataset

To install the braincode_Mouse_Image dataset, run the following commands to move into the "projects" subdirectory under the "conp-dataset" directory (created in the previous step) and run datalad install:

3) Download data from the braincode_Mouse_Image dataset

Now that the dataset has been installed, go into the braincode_Mouse_Image dataset directory.

The files visible after installing the dataset but before downloading (in the next step) are symbolic links and need to be downloaded manually using the datalad get command:

If you run datalad get * command, all the files available in the dataset directory will be downloaded.


For more information on how DataLad works, please visit the DataLad Handbook documentation.