Brain volumes computed with FreeSurfer 6 for all ABIDE I subjects

# ABIDE I FreeSurfer 6 'brain volume' data

This archive contains the following ABIDE I FreeSurfer 6 volumes:
mri/brain.mgz, mri/brain_mask.mgz, mri/aseg.mgz, mri/wm.mgz.

## Credits

This data is derived from the MRI scans of the ABIDE I dataset:

* ABIDE I dataset: https://fcon_1000.projects.nitrc.org/indi/abide/

Quoting from that website:

    "The Autism Brain Imaging Data Exchange I (ABIDE I) represents the first
     ABIDE initiative. Started as a grass roots effort, ABIDE I involved 17
     international sites, sharing previously collected resting state functional
     magnetic resonance imaging (R-fMRI), anatomical and phenotypic datasets
     made available for data sharing with the broader scientific community.
     This effort yielded 1112 dataset, including 539 from individuals with
     ASD and 573 from typical controls (ages 7-64 years, median 14.7 years
     across groups). This aggregate was released in August 2012. Its
     establishment demonstrated the feasibility of aggregating resting
     state fMRI and structural MRI data across sites; the rate of these
     data use and resulting publications (see Manuscripts) have shown its
     utility for capturing whole brain and regional properties of the brain
     connectome in Autism Spectrum Disorder (ASD). In accordance with
     HIPAA guidelines and 1000 Functional Connectomes Project / INDI
     protocols, all datasets have been anonymized, with no protected
     health information included."

Citation: Di Martino, A., Yan, C. G., Li, Q., Denio, E., Castellanos, F. X., Alaerts, K., ... & Milham, M. P. (2014).
          The autism brain imaging data exchange: towards a large-scale evaluation of the intrinsic brain architecture in autism. Molecular psychiatry, 19(6), 659-667.

## How this data was produced

The following steps were used to create the data:

* We downloaded all available MRI scans for the ABIDE I subjects (1035 subjects).
* We pre-processed all subjects in FreeSurfer version 6 (https://freesurfer.net) by running the full recon-all pipeline for each subject.
    - We did not run any quality metrics on the scans or exclude any subjects.

## Contained files

* In order to reduce the size of this dataset, for each subject, we only included the following files:

   - <subject>/mri/brain.mgz: the full brain, in FreeSurfer standard orientation ("conformed")

    - <subject>/mri/brain_mask.mgz: binary mask separating brain from background

    - <subject>/mri/aseg.mgz: brain segmentation, assigning voxels to regions. The region code for the voxel values can be found in the FreeSurferColorLUT.txt file that comes with FreeSurfer 6.

    - <subject>/mri/wm.mgz: binary mask separating white matter from everything else

All files are in FreeSurfer MGZ format.

## What is NOT contained

* The ABIDE demographics information (metadata on the subjects, like age, ...) is not included, you can get it from the ABIDE website.

## Author and License

Note: For the authors of the original ABIDE I dataset, see the Credits section above.

This mri volume data was created by:

    Dr. Tim Schäfer
    Postdoc Computational Neuroimaging
    Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
    University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
    http://rcmd.org/ts

The data is published under the following license:

Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported (CC BY-NC-SA 3.0)

See https://creativecommons.org/licenses/by-nc-sa/3.0/legalcode.txt or the file LICENSE for the full legal code.

See https://creativecommons.org/licenses/by-nc-sa/3.0/ for an easy explanation of what this license means for you.