Debian Science Project
Summary
Neuroscience datasets
Debian Science packages for Neuroscience Datasets

This metapackage will install Debian packages that provide neuroscientific datasets. These datasets can be useful as common data files for applications (e.g. stereotaxic atlases), as example data for online tutorials or teaching, and as input data for analysis algorithms in demonstrations or test suites.

Description

For a better overview of the project's availability as a Debian package, each head row has a color code according to this scheme:

If you discover a project which looks like a good candidate for Debian Science to you, or if you have prepared an unofficial Debian package, please do not hesitate to send a description of that project to the Debian Science mailing list

Links to other tasks

Debian Science Neuroscience datasets packages

Packaging has started and developers might try the packaging code in VCS

Fsl-bangor-cerebellar-atlas
probabilistic atlas of the human cerebellum
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This is a probabilistic atlas of the cerebellar lobules in the anatomical space defined by the MNI152 template. Lobules were masked separately on T1-weighted MRI scans (1 mm isotropic resolution) of 20 healthy young participants (10 male, 10 female, average age 23.7 yrs). These cerebella were then aligned to the standard or non-linear version of the whole-brain MNI152 template using a number of commonly used normalization algorithms, or to a previously published cerebellum-only template (Diedrichsen, J., 2006. A spatially unbiased atlas template of the human cerebellum. NeuroImage 33, 127-138).

This package is part of FSL.

Remark of Debian Science team: This package is waiting for the Debian data package archive to become available.
Fsl-harvard-oxford-atlases
probabilistic atlas of human cortical brain areas (lateralized)
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Probabilistic atlases covering 48 cortical and 21 subcortical structural areas, derived from structural data and segmentations kindly provided by the Harvard Center for Morphometric Analysis.

T1-weighted images of 21 healthy male and 16 healthy female subjects (ages 18-50) were individually segmented using semi-automated tools developed in-house. The T1-weighted images were affine-registered to MNI152 space using FLIRT (FSL), and the transforms then applied to the individual labels. Finally, these were combined across subjects to form population probability maps for each label.

This package is part of FSL.

Remark of Debian Science team: This package is waiting for the Debian data package archive to become available.
Fsl-jhu-dti-whitematter-atlas
human brain white-matter atlas
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There are two white-matter atlases, both kindly provided by Dr. Susumu Mori, Laboratory of Brain Anatomical MRI, Johns Hopkins University.

In the ICBM-DTI-81 white-matter labels atlas, 50 white matter tract labels were created by hand segmentation of a standard-space average of diffusion MRI tensor maps from 81 subjects; mean age 39 (18:59), M:42, F: 39. The diffusion data was kindly provided by the ICBM DTI workgroup.

In the JHU white-matter tractography atlas, 20 structures were identified probabilistically by averaging the results of running deterministic tractography on 28 normal subjects (mean age 29, M:17, F:11).

This package is part of FSL.

Remark of Debian Science team: This package is waiting for the Debian data package archive to become available.
Fsl-juelich-histological-atlas
brain atlas based on cyto- and myelo-architectonic segmentations
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A probabilistic atlas created by averaging multi-subject post-mortem cyto- and myelo-architectonic segmentations, performed by the team of Profs Zilles and Amunts at the Research Center Jülich and kindly provided by Simon Eickhoff.

The atlas contains 32 grey matter structures and 10 white matter structures. This is the same data as used in Eickhoff's Anatomy Toolbox v1.5. The atlas is based on the microscopic and quantitative histological examination of ten human post-mortem brains. The histological volumes of these brains were 3D reconstructed and spatially normalised into the space of the MNI single subject template to create a probabilistic map of each area. For the FSL version of this atlas, these probabilistic maps were then linearly transformed into MNI152 space.

This package is part of FSL.

Remark of Debian Science team: This package is waiting for the Debian data package archive to become available.
Fsl-mni-structural-atlas
hand-segmented single-subject human brain atlas
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9 anatomical structural regions, kindly provided by Jack Lancaster at the Research Imaging Center, UTHSCSA, Texas (originally from the McConnell Brain Imaging Centre, MNI).

A single subject's structural image was hand segmented, and the labels were then propagated to more than 50 subjects' structural images using nonlinear registration. Each resulting labelled brain was then transformed into MNI152 space using affine registration, before averaging segmentations across subjects to produce the final probability images.

This package is part of FSL.

Remark of Debian Science team: This package is waiting for the Debian data package archive to become available.
Fsl-oxford-thalamic-connectivity-atlas
probabilistic brain atlas of thalamic white-matter connectivity
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A probabilistic atlas of 7 sub-thalamic regions, segmented according to their white-matter connectivity to cortical areas, kindly provided by Heidi Johansen-Berg and Timothy Behrens, FMRIB.

This connectivity atlas reports probability of anatomical connection from points in the thalamus to each of 7 cortical zones. These probabilities are calculated using probabilistic diffusion tractography in multiple subjects.

This package is part of FSL.

Remark of Debian Science team: This package is waiting for the Debian data package archive to become available.
Fsl-talairach-daemon-atlas
structural anatomy labels of the Talairach atlas
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A conversion of the original Talairach structural labellings, kindly provided by Jack Lancaster and Diana Tordesillas Gutiérrez at the Research Imaging Center, UTHSCSA, Texas.

This is a digitised version of the original (coarsely sliced) Talairach atlas (Lancaster 2000) after the application of a correcting affine transform (Lancaster 2007) to register it into MNI152 space.

This package is part of FSL.

Remark of Debian Science team: This package is waiting for the Debian data package archive to become available.
Haxby2001-faceobject
face and object processing in ventral temporal cortex (fMRI)
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This is data from a block-design fMRI study on face and object representation in human ventral temporal cortex. The full datasets consists of 6 subjects with 12 runs per subject. In each run, the subjects passively viewed grey scale images of eight object categories, grouped in 24s blocks separated by rest periods. Each image was shown for 500ms and was followed by a 1500ms inter-stimulus interval. Full-brain fMRI data were recorded with a volume repetition time of 2.5s.

This is a meta package that depends on all available subject datasets.

Please cite: James V. Haxby, M. Ida Gobbini, Maura L. Furey, Alumit Ishai, Jennifer L. Schouten and Pietro Pietrini: Distributed and overlapping representations of faces and objects in ventral temporal cortex. (PubMed,eprint) Science 293(5539):2425-2430 (2001)
Remark of Debian Science team: This package is waiting for the Debian data package archive to become

available.

Mclaren-rhesus-macaque-atlas
MRI-based brain atlas of the rhesus macaque monkey
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A population-average MRI-based atlas collection for the rhesus macaque (Macaca mulatta) that can be used with common brain mapping packages such as SPM or FSL. In addition to T1-weighted atlas data, probabilistic tissue classification maps and T2-weighted atlases were also created. Theses atlases are aligned to the MRI volume from the Saleem, K.S. and Logothetis, N.K. (2006) atlas providing an explicit link to histological sections. Additionally, there is a transform to integrate these atlases with the F99 surface-based atlas in CARET.

Please cite: Donald G. McLaren, Kristopher J. Kosmatka, Terrance R. Oakes, Christopher D. Kroenke, Steven G. Kohama, John A. Matochik, Don K. Ingram and Sterling C. Johnson: A Population-Average MRI-Based Atlas Collection of the Rhesus Macaque. (PubMed,eprint) NeuroImage 45(1):52-59 (2009)
Remark of Debian Science team: Upstream agreed to change the license to GPL-3 (might not yet be

reflected on the webpage yet)

Mni-colin27-nifti
Talairach stereotaxic space template
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This template MRI volume was created from 27 T1-weighted MRI scans of a single individual that have been transformed into the Talairach stereotaxic space. The anatomical image is complemented by a brain and a head mask. All images are in 1x1x1 mm resolution.

This package provides the template in NIfTI format.

Please cite: C.J. Holmes, R. Hoge, L. Collins, R. Woods, A.W. Toga and A.C. Evans: Enhancement of MR images using registration for signal averaging. (PubMed) J Comput Assist Tomogr 22(2):324-333 (1998)
Remark of Debian Science team: This package is waiting for the Debian data package archive to become available.
Sri24-atlas
MRI-based brain atlas of normal adult human brain anatomy
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SRI24 is an MRI-based atlas of normal adult human brain anatomy, generated by template-free nonrigid registration from images of 24 normal control subjects.

The atlas comprises T1, T2, and PD weighted structural MRI, tissue probability maps (GM, WM, CSF), maximum-likelihood tissue segmentation, DTI-based measures (FA, MD, longitudinal and transversal diffusivity), and two labels maps of cortical regions and subcortical structures. The atlas is provided at 1mm isotropic image resolution in NIfTI format.

Please cite: Torsten Rohlfing, Natalie M Zahr, Edith V Sullivan and Adolf Pfefferbaum: The SRI24 multichannel atlas of normal adult human brain structure. (PubMed) Human Brain Mapping 31(5):798-819 (2010)
Remark of Debian Science team: This package is waiting for the Debian data package archive to become

available.

Unofficial packages built by somebody else

Mni-icbm152-nlin-2009
MNI stereotaxic space human brain template
Responsible: NeuroDebian team
License: custom, DFSG-compliant

This is an unbiased standard magnetic resonance imaging template volume for the normal human population. It has been created by the Montreal Neurological Institute (MNI) using anatomical data from the International Consortium for Brain Mapping (ICBM).

The package provides a 1x1x1 mm and 0.5x0.5x0.5 mm resolution templates (hemissphere-symetric and asymetric non-linearily co-registered versions), some including T1w, T2w, PDw modalities, T2 relaxometry, and tissue probability maps. In addition, it contains a lobe atlas, and masks for brain, eyes and face.

Please cite: V.S. Fonov, A.C. Evans, R.C. McKinstry, C.R. Almli and D.L. Collins: Unbiased nonlinear average age-appropriate brain templates from birth to adulthood. (2009)
Remark of Debian Science team: This package is waiting for the Debian data package archive to become available.
*Popularitycontest results: number of people who use this package regularly (number of people who upgraded this package recently) out of 203532