Local Gyrification Index computed with FreeSurfer 6 for all ABIDE I subjects

# ABIDE I FreeSurfer 6 'local gyrification index' (lGI) data

DOI of this dataset: 10.5281/zenodo.7132610

This directory 'abide_freesurfer6_lgi' contains the ABIDE I FreeSurfer 6 'local gyrification index' (lGI) data and meshes.

## 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.
* We computed pial-lgi (Schaer et al. 2008, https://doi.org/10.1109/TMI.2007.903576) as implemented in FreeSurfer 6 for all subjects.
    - For some of the subjects, MRI data was not available or lgi could not be computed due to very bad quality of the (or a completely failed) surface reconstruction. These subjects are listed in the file 'subjects_lgi_computation_failed.txt' (14 of 1035 subjects).
    - All subjects for which lgi computation succeeded for both hemispheres are listed in the file 'subjects.txt' (1021 of 1035 subjects).

## Contained files

* In order to reduce the size of this dataset, for each subject, we only included the following files:
    - <subject>/surf/lh.pial      : the pial surface mesh for the left hemisphere, in FreeSurfer surf format.
    - <subject>/surf/rh.pial      : the pial surface mesh for the right hemisphere, in FreeSurfer surf format.
    - <subject>/surf/lh.pial_lgi  : the per-vertex lgi values for the left hemisphere, in FreeSurfer curv format.
    - <subject>/surf/rh.pial_lgi  : the per-vertex lgi values for the right hemisphere, in FreeSurfer curv format.

See the section 'How this data was produced' for information on the files 'subjects.txt' and 'subjects_lgi_computation_failed.txt'.

## 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.
* The lgi values are only contained in native space. Standard space data is available as a separate download on Zenodo.

## Author and License

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

This lgi 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.