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https://github.com/dfsp-spirit/abide_preproc_smri_freesurfer6

Data from our own pre-processing of the ABIDE I sMRI dataset (1035 subjects) in FreeSurfer v6.
https://github.com/dfsp-spirit/abide_preproc_smri_freesurfer6

abide-data brain brain-imaging computational-neuroimaging dataset derived-data freesurfer mri

Last synced: 3 days ago
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Data from our own pre-processing of the ABIDE I sMRI dataset (1035 subjects) in FreeSurfer v6.

Host: GitHub
URL: https://github.com/dfsp-spirit/abide_preproc_smri_freesurfer6
Owner: dfsp-spirit
Created: 2022-11-13T10:54:39.000Z (about 2 years ago)
Default Branch: main
Last Pushed: 2023-06-29T10:32:04.000Z (over 1 year ago)
Last Synced: 2024-10-31T18:12:08.480Z (about 2 months ago)
Topics: abide-data, brain, brain-imaging, computational-neuroimaging, dataset, derived-data, freesurfer, mri
Homepage:
Size: 1.7 MB
Stars: 6
Watchers: 2
Forks: 0
Open Issues: 1
Metadata Files:
- Readme: README.md

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README

# abide_preproc_smri_freesurfer6
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.

## About

This is pre-processed structural magnetic resonance imaging (sMRI) data from the [ABIDE I dataset](https://fcon_1000.projects.nitrc.org/indi/abide/abide_I.html). In short, we downloaded all 1035 ABIDE I subjects and ran their brain scans through [FreeSurfer v6](https://freesurfer.net/) `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](https://github.com/dfsp-spirit/abide_preproc_smri_freesurfer6/issues) in that case.

## Available data

The following data is available:

### Aggregated stats (by subject, aggregated over atlas regions)

The following aggregated stats were generated by us using `aparcstats2table`, with our [parallel_anatomical_stats scripts](https://github.com/dfsp-spirit/freesurfer_parallel_scripts/tree/main/tools).

* aggregated aparc stats (based on cortical parcellations):
- for the Desikan atlas: thickness, area, volume
- see see [stats/ directory](./stats/)
* aggregated aparc.a2009s stats (based on cortical parcellations):
- for the Destrieux atlas: thickness, area, volume
- see see [stats/aparc.a2009s/ directory](./stats/aparc.a2009s)
* aggregated aseg stats (based on volume segmentation):
- aseg stats, see [stats directory ](./stats/)

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](https://github.com/dfsp-spirit/freesurfer_parallel_scripts/). 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 [stats/brainvol/ directory](./stats/brainvol/).

### Local Gyrification Index (lGI)

See the [native space lgi data for all ABIDE I subjects](https://doi.org/10.5281/zenodo.7132610) on Zenodo (6.5 GB download).