Data from our own pre-processing of the ABIDE I sMRI dataset (1035 subjects) in FreeSurfer v6.
Make sure to read and understand the license before using the data in this repository.
This is pre-processed structural magnetic resonance imaging (sMRI) data from the ABIDE I dataset. In short, we downloaded all 1035 ABIDE I subjects and ran their brain scans through FreeSurfer v6 recon-all and related tools (aseg stats, aparc start, lGI computation). The full size of the dataset is 790 GB, so we make it available in chunks.
The uploaded archives are very large already (> 30 GB), so we opted not to upload log files, temporary files and other parts of the FreeSurfer 6 output which are not relevant for neuroimaging research. We have the full data though, and if you feel you require a file that is missing, we can add that file for all subjects in another upload. Please get in touch by opening an issue in that case.
The following data is available:
The following aggregated stats were generated by us using aparcstats2table, with our parallel_anatomical_stats scripts.
- aggregated aparc stats (based on cortical parcellations):
- for the Desikan atlas: thickness, area, volume
- see see stats/ directory
- aggregated aparc.a2009s stats (based on cortical parcellations):
- for the Destrieux atlas: thickness, area, volume
- see see stats/aparc.a2009s/ directory
- aggregated aseg stats (based on volume segmentation):
- aseg stats, see stats directory
The following information on the volume of various brain regions was generated by us by parsing parts of the aseg/aparc stats and running mris_anatomical_stats, implemented in our extract_total_brain_measures.bash script. We tried to give expressive names to the columns, but if in doubt, check the script to see how exactly a certain column was computed. These are typically used as covariates to control for in statistical analyses, along with demographical information on the subject (which is available on the ABIDE website as a CSV file).
- total brain volume and related volume measurements:
See the native space lgi data for all ABIDE I subjects on Zenodo (6.5 GB download).
It includes the following files for each subject:
<subject>/surf/lh.pial<subject>/surf/rh.pial<subject>/surf/lh.pial_lgi<subject>/surf/rh.pial_lgi
See the surface descriptor data for all ABIDE I subjects on Zenodo (6.1 GB download).
It includes the following files for each subject:
<subject>/surf/lh.thickness<subject>/surf/rh.thickness<subject>/surf/lh.area<subject>/surf/rh.area<subject>/surf/lh.volume<subject>/surf/rh.volume<subject>/surf/lh.curv<subject>/surf/rh.curv<subject>/surf/lh.sulc<subject>/surf/rh.sulc<subject>/surf/lh.jacobian_white<subject>/surf/rh.jacobian_white
See the brain surfaces for all ABIDE I subjects on Zenodo (16.3 GB download).
It includes the following files for each subject:
<subject>/surf/lh.white<subject>/surf/rh.white<subject>/surf/lh.orig<subject>/surf/rh.orig<subject>/surf/lh.sphere<subject>/surf/rh.sphere
Note: The pial surface files are part of the Local Gyrification Index dataset, see above.
See the labels for all ABIDE I subjects on Zenodo (4.7 GB download).
It includes the following files for each subject:
<subject>/label/lh.cortex.label<subject>/label/rh.cortex.label<subject>/label/lh.aparc.annot<subject>/label/rh.aparc.annot<subject>/label/lh.aparc.a2009s.annot<subject>/label/rh.aparc.a2009s.annot
See the Brain volumnes for all ABIDE I subjects on Zenodo (3.1 GB download).
It includes the following files for each subject:
<subject>/mri/brain.mgz<subject>/mri/brain_mask.mgz<subject>/mri/aseg.mgz<subject>/mri/wm.mgz
See the Surface transforms for all ABIDE I subjects on Zenodo (5.5 GB download).
It includes the following files for each subject:
<subject>/surf/lh.sphere.reg<subject>/surf/rh.sphere.reg
These files are required if you want to map surface-based data between subjects (including template subjects).
This package contains aggregated data derived from the ABIDE I data set. That data is published under a Creative Commons, Attribution-NonCommercial-Share Alike License as explained in the ABIDE I Usage Agreement.
Please cite the relevant ABIDE I papers when using the data for scientific publications, especially the ABIDE I Announcing Manuscript by Di Martino et al.