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The Connectome Viewer is released under the Modified BSD license. See the license page for details.

Connectome File Format - Datasets (Version 2.0)

The Connectome File Format enables pooling of multi-modal neuroimaging datasets and metadata annotation. All data files and a metadata XML file (meta.cml) are packaged in one ZIP file with file name ending .cff for convenient data distribution. To work with these files, just unzip the .cff files, load the meta.cml file through the cfflib package. The Python library cfflib enables reading, writing and manipulation of connectome files - here are installation instructions and tutorials. Furthermore, the Connectome Viewer Toolkit can read .cff files or meta.cml files using cfflib. The following connectome files are also under version control on GitHub.

connectome0001 - tp1

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An exemplary output of a Diffusion Spectrum Imaging dataset processed by the Connectome Mapper. The raw data is here.

Human cortex connectivity dataset

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Reference: Hagmann P, Cammoun L, Gigandet X, Meuli R, Honey CJ, et al. 2008 Mapping the Structural Core of Human Cerebral Cortex. PLoS Biol 6(7): e159. doi:10.1371/journal.pbio.0060159
Connection matrices and anatomical labels for areas of the human cerebral cortex. These data were generated by DSI (diffusion spectrum imaging) of 5 participants. Participant A was scanned twice. Note that these connection matrices are weighted and symmetric (undirected).

Single subject connectivity

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This file contains connectivity data for a single subject as done with the Connectome Mapping Toolbox developed at EPFL.

Freesurfer Atlas with Average Connectivity

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This atlas is also known as the 'Desikan-Killiany' cortical atlas. It is a gyral based atlas: ie, a gyrus was defined as running between the bottoms of two adjacent sulci. That is, a gyrus includes the part visible on the pial view + adjacent banks of the sulci limiting this gyrus.

The atlas is enriched by an avarage connectivity dataset: Parameters: DSI 258 diffusion gradients over a hemisphere with bmax=8000 s/mm2 Voxel size 2.2 x 2.2 x 3 mm3 Data processed according to Hagmann P, Cammoun L, Gigandet X, Meuli R, Honey CJ, et al. 2008 Mapping the Structural Core of Human Cerebral Cortex. PLoS Biol 6(7): e159. doi:10.1371journal.pbio.0060159 20 healthy subjects aged between 22 and 33 years, males and females

Macaque connectivity Right Hemisphere

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Hagmann P, Cammoun L, Gigandet X, Meuli R, Honey CJ, et al. 2008 Mapping the Structural Core of Human Cerebral Cortex. PLoS Biol 6(7): e159. doi:10.1371/journal.pbio.0060159
The macaque dataset used for the study. See references.

C.elegans connectivity

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C. elegans global network of 277 neurons and 131 frontal neurons. The files include the matrix, labels of the neurons, and the spatial positions of the neurons as two-dimensional coordinates (unit is mm).

2 Functional Connectome (fMRI) datasets

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This Connectome File exposes data from two subjects from the Baltimore Dataset of the 1000 Functional Connectomes Project. Metadata, anatomical and functional MRI data is included.

pbc2009icdm brain 1

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For more information, seeCompetition: PBC BCC Fall 2009, IEEE ICDM

SRI24 Atlas - Normal Adult 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 the following channels of information: T1 (T1.nii.gz), T2 (T2.nii.gz), and proton density-weighted (PD.nii.gz) structural MRI, their unstripped coutnerparts, tissue probability maps (GM, WM, CSF), maximum-likelihood tissue segmentation, DTI-based measures (FA, MD, longitudinal ("l1") and transversal ("lt") diffusivity), and two parcellation maps for with cortical regions and subcortical structures.

The atlas is provided at 1mm isotropic image resolution and is based on 3T MR data.

fsaverage surfaces

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For more information, see

SPL-PNL Brain Atlas

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The initial version of the SPL-PNL Brain Atlas was developed by the Surgical Planning Laboratory in collaboration with the Harvard Neuroscience Laboratory at Brockton VA Medical Center. Dr. Martha Shenton, one of the original people involved with the Harvard Neuroscience Laboratory, is now the Director of the Psychiatry Neuroimaging Laboratory (PNL), Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School.
The atlas was derived from a volumetric T1-weighted MR-scan of a healthy volunteer, using semi-automated image segmentation and three-dimensional reconstruction techniques. Over the years, the original atlas has undergone several revisions. The current version consists of:
1. the original volumetric whole brain MRI of a healthy volunteer;
2. a set of detailed label maps;
3. 160+ three-dimensional models of the labeled anatomical structures;
The SPL-PNL Brain Atlas provides important reference information for surgical planning. It has been used for template-driven segmentation and also as a powerful neuroanatomy teaching tool. We are pleased to make this brain atlas available to our colleagues for free download. Please note that the data is being distributed under the Slicer license. By downloading these data, you agree to acknowledge our contribution in any of your publications that result form the use of this atlas. Please acknowledge the following grants: P41 RR13218, R01 MH050740.

Example dataset

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This file contains a show of the multi-modal files hostable by this format.