DOI: 10.5281/zenodo.7132610
title: Local Gyrification Index computed with FreeSurfer 6 for all ABIDE I subjects

description: # 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. <br> ## 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<br> ABIDE initiative. Started as a grass roots effort, ABIDE I involved 17<br> international sites, sharing previously collected resting state functional<br> magnetic resonance imaging (R-fMRI), anatomical and phenotypic datasets<br> made available for data sharing with the broader scientific community.<br> This effort yielded 1112 dataset, including 539 from individuals with<br> ASD and 573 from typical controls (ages 7-64 years, median 14.7 years<br> across groups). This aggregate was released in August 2012. Its<br> establishment demonstrated the feasibility of aggregating resting<br> state fMRI and structural MRI data across sites; the rate of these<br> data use and resulting publications (see Manuscripts) have shown its<br> utility for capturing whole brain and regional properties of the brain<br> connectome in Autism Spectrum Disorder (ASD). In accordance with<br> HIPAA guidelines and 1000 Functional Connectomes Project / INDI<br> protocols, all datasets have been anonymized, with no protected<br> health information included." Citation: Di Martino, A., Yan, C. G., Li, Q., Denio, E., Castellanos, F. X., Alaerts, K., ... & Milham, M. P. (2014).<br> 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).<br> * We pre-processed all subjects in FreeSurfer version 6 (https://freesurfer.net) by running the full recon-all pipeline for each subject.<br> - We did not run any quality metrics on the scans or exclude any subjects.<br> * We computed pial-lgi (Schaer et al. 2008, https://doi.org/10.1109/TMI.2007.903576) as implemented in FreeSurfer 6 for all subjects.<br> - 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).<br> - All subjects for which lgi computation succeeded for both hemispheres are listed in the file 'subjects.txt' (1021 of 1035 subjects). <br> ## Contained files * In order to reduce the size of this dataset, for each subject, we only included the following files:<br> - &lt;subject&gt;/surf/lh.pial : the pial surface mesh for the left hemisphere, in FreeSurfer surf format.<br> - &lt;subject&gt;/surf/rh.pial : the pial surface mesh for the right hemisphere, in FreeSurfer surf format.<br> - &lt;subject&gt;/surf/lh.pial_lgi : the per-vertex lgi values for the left hemisphere, in FreeSurfer curv format.<br> - &lt;subject&gt;/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.<br> * 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<br> Postdoc Computational Neuroimaging<br> Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy<br> University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany<br> 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.