What is the difference between brain parcellation and brain segmentation? (question based on Freesurfer that produces parcellation volume and segmentation volume measures)


3 Answers 3


Brain Parcellation in Freesurfer is splitting images of the brain into their defined partitions, mapping the brain

Brain Parcellation Images Brain Parcellation images from Eickhoff et al. (2018)

Thyreau & Taki (2020) points out:

The parcellation of the human cortex into meaningful anatomical units is a common step of various neuroimaging studies. There have been multiple successful efforts to process magnetic resonance (MR) brain images automatically and identify specific anatomical regions, following atlases defined from cortical landmarks. Those definitions usually rely first on a high-quality brain surface reconstruction. On the other hand, when high accuracy is not a requirement, simpler methods based on warping a probabilistic atlas have been widely adopted.

Brain Segmentation

Brain segmentation initially involves the removal of non-cerebral tissues like skull. But, segmentation is also (Despotović, et al. 2015)

commonly used for measuring and visualizing the brain's anatomical structures, for analyzing brain changes, for delineating pathological regions, and for surgical planning and image-guided interventions. In the last few decades, various segmentation techniques of different accuracy and degree of complexity have been developed and reported in the literature.

Image of segmented brain Image from Lee et al. (2020)

McClure et al. (2019) describes

a Bayesian deep neural network (DNN) for predicting FreeSurfer segmentations of structural MRI volumes, in minutes rather than hours.


Despotović, I., Goossens, B., & Philips, W. (2015). MRI segmentation of the human brain: challenges, methods, and applications. Computational and mathematical methods in medicine, 2015, 450341. https://doi.org/10.1155/2015/450341

Eickhoff, S. B., Yeo, B. T., & Genon, S. (2018). Imaging-based parcellations of the human brain. Nature Reviews Neuroscience, 19(11), 672-686. https://doi.org/10.1038/s41583-018-0071-7

Lee B, Yamanakkanavar N, Choi JY (2020). Automatic segmentation of brain MRI using a novel patch-wise U-net deep architecture. PLoS ONE 15(8): e0236493. https://doi.org/10.1371/journal.pone.0236493

McClure, P., Rho, N., Lee, J. A., Kaczmarzyk, J. R., Zheng, C. Y., Ghosh, S. S., ... & Pereira, F. (2019). Knowing what you know in brain segmentation using Bayesian deep neural networks. Frontiers in neuroinformatics, 13, 67. https://doi.org/10.3389/fninf.2019.00067

Thyreau, B., & Taki, Y. (2020). Learning a cortical parcellation of the brain robust to the MRI segmentation with convolutional neural networks. Medical image analysis, 61, 101639. https://doi.org/10.1016/j.media.2020.101639


Segmentation is about tissue type and anatomical structures. It's mainly concerned with identifying the voxels of brain and cerebellum, separating gray matter and white matter, identifying subcortical structures such as the hippocampus, etc. It's typically volumes, rather than surfaces, that come up in this context.

Parcellation is about neuroanatomy. It's mainly concerned with defining regions based on architectonics, connectivity, function, or topography. Think "primary visual cortex," "Broca's area," etc. It's typically surfaces, rather than volumes, that come up in this context.

(The other answer is fine -- I am just adding a short and more direct answer to the question.)


Brain parcellation and brain segmentation are related, but different, approaches to analyzing the structure of the brain.

Brain parcellation refers to the process of dividing the brain into distinct, non-overlapping regions, or parcels, based on functional, structural, or connectivity criteria. This division results in a parcellation map, which assigns a unique label to each parcel, indicating its functional or structural identity. In Freesurfer, the parcellation volume is a map that assigns a unique label to each voxel in the brain, indicating its parcel membership.

Brain segmentation, on the other hand, refers to the process of dividing the brain into distinct, non-overlapping regions based on the tissue type (i.e. gray matter, white matter, or cerebrospinal fluid). The result of segmentation is a segmentation map, which assigns a unique label to each voxel in the brain, indicating its tissue type. In Freesurfer, the segmentation volume is a map that assigns a unique label to each voxel in the brain, indicating its tissue type.

So, in short, brain parcellation aims to divide the brain into functional or structural regions, while brain segmentation aims to divide the brain into tissue types.

  • 1
    $\begingroup$ Welcome. Can you add citations and/or resources so others can background read on your answer? $\endgroup$
    – AliceD
    Feb 8, 2023 at 12:37

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