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Connectome Mapping Toolkit specifications


Unique identifier OMICS_10609
Name Connectome Mapping Toolkit
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability No
Maintained Yes


No version available


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Publication for Connectome Mapping Toolkit

Connectome Mapping Toolkit citations


The Energy Landscape of Neurophysiological Activity Implicit in Brain Network Structure

Sci Rep
PMCID: 5802783
PMID: 29410486
DOI: 10.1038/s41598-018-20123-8

[…] Anatomical scans were segmented using FreeSurfer and parcellated according to the Lausanne 2008 atlas included in the connectome mapping toolkit. A parcellation scheme including 234 regions was registered to the B0 volume from each subject’s DSI data. The B0 to MNI voxel mapping produced via QSDR was used to map regi […]


Stochastic resonance at criticality in a network model of the human cortex

Sci Rep
PMCID: 5638949
PMID: 29026142
DOI: 10.1038/s41598-017-13400-5

[…] maximum b-value 8,000 s/mm 2, and 2.2 × 2.2 × 3.0 mm voxel size. EPI sequence was 3.3-mm in-plane resolution and 3.3-mm slice thickness with TR 1,920 ms. DSI and MPRAGE data were processed using the Connectome Mapping Toolkit. Each participant’s gray and white matter compartments were segmented from the MPRAGE volume. The gray matter volume was subdivided into 68 cortical and 15 subcortical anato […]


Exploring the role of white matter connectivity in cortex maturation

PLoS One
PMCID: 5435226
PMID: 28545040
DOI: 10.1371/journal.pone.0177466
call_split See protocol

[…] n Toolkit [], with the gradient table updated for the rigid-body registration performed earlier. Whole brain tractography was performed using the deterministic streamline algorithm implemented in the Connectome Mapping Toolkit [,] and using standard parameters. 32 streamlines were initiated in each WM voxel and propagated along the two opposite directions given by the local tensor orientation. Str […]


Imaging analysis of Parkinson’s disease patients using SPECT and tractography

Sci Rep
PMCID: 5128922
PMID: 27901100
DOI: 10.1038/srep38070

[…] mage were used as input to the PVC algorithm for voxel-wise partial volume effect correction. The raw MRI data were pre-processed using the following steps. MRI pre-processing was performed using the Connectome Mapping Toolkit (CMTK) and Python-based open-source software ( For each subject, a T2-weighted image was used in an intermediate step to achieve image co-registration between […]


Impaired fornix–hippocampus integrity is linked to peripheral glutathione peroxidase in early psychosis

PMCID: 5545707
PMID: 27459724
DOI: 10.1038/tp.2016.117

[…] All images were visually inspected for artifacts or structural abnormalities. Diffusion and T1-weighted MRI data were processed using the Connectome Mapping Toolkit (, , MPRAGE volumes were segmented into white matter, gray matter and cerebrospinal fluid compartments, and were linearly registered to the b0 volume. […]


Brain network characterization of high risk preterm born school age children

PMCID: 4761723
PMID: 26955515
DOI: 10.1016/j.nicl.2016.02.001

[…] The extraction of the whole brain structural connectivity matrices (connectomes) for each subject was performed using the Connectome Mapping Toolkit, a python-based open-source software that implements a full diffusion MRI processing pipeline, from raw diffusion/T1/T2 data to multi-resolution connection matrices (www.cmt […]


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Connectome Mapping Toolkit institution(s)
Signal Processing Laboratory 5, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland; Department of Radiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland

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