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Philip Cook edited this page Feb 25, 2020 · 41 revisions

A number of different labeling systems are available for obtaining summary measures.

  • Processing derived
    • antsct: the classes from the 6-class segmentation step in the ANTs pipeline
    • brain: the volume of the generated brain mask image (NOT total intracranial volume)
  • Joint label fusion
    • brainCOLOR mindboggle: labels obtained from the joint label fusion (JLF) pipeline, they include both cortical and non-cortical structures. The meta-info is found in the "braincolorLabels" and "braincolorLabelsExtended" data.frames that are included in QuANTs. The 'Extended' contains info for labels that do not appear in our pipeline, but are technically part of the protocol.
  • Systems defined in MNI152 space
    • jhuLabels: white matter labels defined manually
    • jhuTracts: white matter labels defined via tractography
    • glasser360
    • midevel
    • schaefer100/200/400
  • Other
    • mristudio: multi-atlas white matter segmentation

Systems derived from processing pipeline

antsct

Includes 6 labels

  1. CSF
  2. Cortex
  3. White matter
  4. Deep Gray
  5. Brainstem
  6. Cerebellum

A few notes

  • The labels for deep gray and brainstem are really just different versions of "not-cortex" and should not be used to any analyses
  • The values for cortex have been refined using the cortical thickness maps that the pipeline produces. Any voxel with zero thickness is excluded to obtain a more accurate cortical segmentation.
  • Volumes are reported for all regions and thickness is reported for the cortex label

six tissue image

Tustison, Nicholas J., et al. "Large-scale evaluation of ANTs and FreeSurfer cortical thickness measurements." Neuroimage 99 (2014): 166-179.

@article{tustison2014large, title={Large-scale evaluation of ANTs and FreeSurfer cortical thickness measurements}, author={Tustison, Nicholas J and Cook, Philip A and Klein, Arno and Song, Gang and Das, Sandhitsu R and Duda, Jeffrey T and Kandel, Benjamin M and van Strien, Niels and Stone, James R and Gee, James C and others}, journal={Neuroimage}, volume={99}, pages={166--179}, year={2014}, publisher={Elsevier} }

brain

Not much to this one, just the volume of the brainmask produced by antsBrainExtraction.sh. NOTE: I believe we are using a customized version of this script that varies from the official version in the repo so this should be noted.

Tustison, Nicholas J., et al. "Large-scale evaluation of ANTs and FreeSurfer cortical thickness measurements." Neuroimage 99 (2014): 166-179.

@article{tustison2014large, title={Large-scale evaluation of ANTs and FreeSurfer cortical thickness measurements}, author={Tustison, Nicholas J and Cook, Philip A and Klein, Arno and Song, Gang and Das, Sandhitsu R and Duda, Jeffrey T and Kandel, Benjamin M and van Strien, Niels and Stone, James R and Gee, James C and others}, journal={Neuroimage}, volume={99}, pages={166--179}, year={2014}, publisher={Elsevier} }

Joint label fusion label sets

mindboggle brainCOLOR

This is the "main" labeling system that we use. It includes 134 unique labels, 98 of which are cortical regions (homologous regions in right and left hemispheres have separate labels). In our pipeline, the cortical labels are masked to only include voxels with a non-zero cortical thickness. Previously we were referring to this as the "mindboggle" labels, but this can lead to confusion as the mindboggle project developed multiple labeling systems (see link below) and the cortical only DKT labeling is perhaps more widely recognized. To avoid confusion we will henceforth refer to the whole-brain labels as the brainCOLOR labels.

More info

brainCOLOR image

Klein, Arno, et al. "Open labels: online feedback for a public resource of manually labeled brain images." 16th Annual Meeting for the Organization of Human Brain Mapping. 2010.

@inproceedings{klein2010open, title={Open labels: online feedback for a public resource of manually labeled brain images}, author={Klein, Arno and Dal Canton, Tito and Ghosh, Satrajit S and Landman, Bennett and Lee, Joel and Worth, Andrew}, booktitle={16th Annual Meeting for the Organization of Human Brain Mapping}, year={2010} }

Label systems defined in MNI152 space

midevel

These subcortical structures are defined in MNI152 space. Need clarification on where these labels came from. I believe this is a hybrid of multiple protocols, but I don't know the origin.

midevel image

jhuLabels

"JHU labels as distributed with FSL." These white matter labels are defined in MNI152 space.

jhuLabels image

Reference: Reproducibility of quantitative tractography methods applied to cerebral white matter

FSL reference:

Smith, Stephen M., et al. "Advances in functional and structural MR image analysis and implementation as FSL." Neuroimage 23 (2004): S208-S219.

@article{smith2004advances, title={Advances in functional and structural MR image analysis and implementation as FSL}, author={Smith, Stephen M and Jenkinson, Mark and Woolrich, Mark W and Beckmann, Christian F and Behrens, Timothy EJ and Johansen-Berg, Heidi and Bannister, Peter R and De Luca, Marilena and Drobnjak, Ivana and Flitney, David E and others}, journal={Neuroimage}, volume={23}, pages={S208--S219}, year={2004}, publisher={Elsevier} }

jhuTracts

"JHU tracts as distributed with FSL."

Reference:

Tract probability maps in stereotaxic spaces: analyses of white matter anatomy and tract-specific quantification

FSL reference:

Smith, Stephen M., et al. "Advances in functional and structural MR image analysis and implementation as FSL." Neuroimage 23 (2004): S208-S219.

@article{smith2004advances, title={Advances in functional and structural MR image analysis and implementation as FSL}, author={Smith, Stephen M and Jenkinson, Mark and Woolrich, Mark W and Beckmann, Christian F and Behrens, Timothy EJ and Johansen-Berg, Heidi and Bannister, Peter R and De Luca, Marilena and Drobnjak, Ivana and Flitney, David E and others}, journal={Neuroimage}, volume={23}, pages={S208--S219}, year={2004}, publisher={Elsevier} }

glasser360

glasser360 image

Glasser, Matthew F., et al. "A multi-modal parcellation of human cerebral cortex." Nature 536.7615 (2016): 171.

@article{Glasser_2016, doi = {10.1038/nature18933}, url = {https://doi.org/10.1038%2Fnature18933}, year = 2016, month = {jul}, publisher = {Springer Nature}, volume = {536}, number = {7615}, pages = {171--178}, author = {Matthew F. Glasser and Timothy S. Coalson and Emma C. Robinson and Carl D. Hacker and John Harwell and Essa Yacoub and Kamil Ugurbil and Jesper Andersson and Christian F. Beckmann and Mark Jenkinson and Stephen M. Smith and David C. Van Essen}, title = {A multi-modal parcellation of human cerebral cortex}, journal = {Nature} }

schaefer100

schaefer100 image

Schaefer, Alexander, et al. "Local-global parcellation of the human cerebral cortex from intrinsic functional connectivity MRI." Cerebral Cortex 28.9 (2017): 3095-3114.

Thomas Yeo, B. T., et al. "The organization of the human cerebral cortex estimated by intrinsic functional connectivity." Journal of neurophysiology 106.3 (2011): 1125-1165.

@article{Schaefer_2017, doi = {10.1093/cercor/bhx179}, url = {https://doi.org/10.1093%2Fcercor%2Fbhx179}, year = 2017, month = {jul}, publisher = {Oxford University Press ({OUP})}, pages = {1--20}, author = {Alexander Schaefer and Ru Kong and Evan M. Gordon and Timothy O. Laumann and Xi-Nian Zuo and Avram J. Holmes and Simon B. Eickhoff and B.T. Thomas Yeo}, title = {Local-Global Parcellation of the Human Cerebral Cortex from Intrinsic Functional Connectivity {MRI}}, journal = {Cerebral Cortex} }

@article{Thomas_Yeo_2011, doi = {10.1152/jn.00338.2011}, url = {https://doi.org/10.1152%2Fjn.00338.2011}, year = 2011, month = {jun}, publisher = {American Physiological Society}, volume = {106}, number = {3}, pages = {1125--1165}, author = {B. T. Thomas Yeo and F. M. Krienen and J. Sepulcre and M. R. Sabuncu and D. Lashkari and M. Hollinshead and J. L. Roffman and J. W. Smoller and L. Zollei and J. R. Polimeni and B. Fischl and H. Liu and R. L. Buckner}, title = {The organization of the human cerebral cortex estimated by intrinsic functional connectivity}, journal = {Journal of Neurophysiology} }

schaefer200

schaefer200 image

Schaefer, Alexander, et al. "Local-global parcellation of the human cerebral cortex from intrinsic functional connectivity MRI." Cerebral Cortex 28.9 (2017): 3095-3114.

Thomas Yeo, B. T., et al. "The organization of the human cerebral cortex estimated by intrinsic functional connectivity." Journal of neurophysiology 106.3 (2011): 1125-1165.

@article{Schaefer_2017, doi = {10.1093/cercor/bhx179}, url = {https://doi.org/10.1093%2Fcercor%2Fbhx179}, year = 2017, month = {jul}, publisher = {Oxford University Press ({OUP})}, pages = {1--20}, author = {Alexander Schaefer and Ru Kong and Evan M. Gordon and Timothy O. Laumann and Xi-Nian Zuo and Avram J. Holmes and Simon B. Eickhoff and B.T. Thomas Yeo}, title = {Local-Global Parcellation of the Human Cerebral Cortex from Intrinsic Functional Connectivity {MRI}}, journal = {Cerebral Cortex} }

@article{Thomas_Yeo_2011, doi = {10.1152/jn.00338.2011}, url = {https://doi.org/10.1152%2Fjn.00338.2011}, year = 2011, month = {jun}, publisher = {American Physiological Society}, volume = {106}, number = {3}, pages = {1125--1165}, author = {B. T. Thomas Yeo and F. M. Krienen and J. Sepulcre and M. R. Sabuncu and D. Lashkari and M. Hollinshead and J. L. Roffman and J. W. Smoller and L. Zollei and J. R. Polimeni and B. Fischl and H. Liu and R. L. Buckner}, title = {The organization of the human cerebral cortex estimated by intrinsic functional connectivity}, journal = {Journal of Neurophysiology} }

schaefer400

schaefer400 image

Schaefer, Alexander, et al. "Local-global parcellation of the human cerebral cortex from intrinsic functional connectivity MRI." Cerebral Cortex 28.9 (2017): 3095-3114.

Thomas Yeo, B. T., et al. "The organization of the human cerebral cortex estimated by intrinsic functional connectivity." Journal of neurophysiology 106.3 (2011): 1125-1165.

@article{Schaefer_2017, doi = {10.1093/cercor/bhx179}, url = {https://doi.org/10.1093%2Fcercor%2Fbhx179}, year = 2017, month = {jul}, publisher = {Oxford University Press ({OUP})}, pages = {1--20}, author = {Alexander Schaefer and Ru Kong and Evan M. Gordon and Timothy O. Laumann and Xi-Nian Zuo and Avram J. Holmes and Simon B. Eickhoff and B.T. Thomas Yeo}, title = {Local-Global Parcellation of the Human Cerebral Cortex from Intrinsic Functional Connectivity {MRI}}, journal = {Cerebral Cortex} }

@article{Thomas_Yeo_2011, doi = {10.1152/jn.00338.2011}, url = {https://doi.org/10.1152%2Fjn.00338.2011}, year = 2011, month = {jun}, publisher = {American Physiological Society}, volume = {106}, number = {3}, pages = {1125--1165}, author = {B. T. Thomas Yeo and F. M. Krienen and J. Sepulcre and M. R. Sabuncu and D. Lashkari and M. Hollinshead and J. L. Roffman and J. W. Smoller and L. Zollei and J. R. Polimeni and B. Fischl and H. Liu and R. L. Buckner}, title = {The organization of the human cerebral cortex estimated by intrinsic functional connectivity}, journal = {Journal of Neurophysiology} }

WIPs - candidate label systems being explored

mristudio

Unable to determine the protocol used to generate these labels, so not recommended for now.

"Data were obtained as a courtesy of Dr. Mori (www.mristudio.org) in Johns Hopkins University"

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