11.1.4. Macaque atlas: the CHARM

Charm is more valuable than beauty. You can resist beauty, but you can’t resist charm. –Audrey Tautou


Here we present the Cortical Hierarchy Atlas of the Rhesus Macaque (CHARM).

This atlas is defined in the coordinates/space of the NMT v2 template, described here:


The CHARM parcellates the macaque cortex at six spatial scales. The finest level is based on the D99 atlas, while the broadest level forms four cortical lobes. Between these levels, regions are progressively grouped to form increasingly large composite structures. This allows the researcher to choose the appropriate scale of investigation for their study design and data.

Example of the CHARM hierarchical structure

Tree diagram showing successively finer parcellation of the inferior temporal cortex (from Jung et al., 2021)


The CHARM is distributed as a single data set with six sub-volumes. Note that for the purpose of using AFNI sub-brick selectors, CHARM Level 1 is volume "[0]" and Level 6 is volume "[5]", because AFNI (like Python and C) use zero-base counting.

The CHARM is distributed with the NMT v2. The NMT v2 has several forms and variants (based on symmetry/asymmetry, FOV and voxel size), and for each of these there is an accompanying CHARM.

Note that the NMT download also includes a CSV table file of the ROI labels, hierarchically organized. This can be viewed as a simple text file or within any spreadsheet software, such as shown in the following image.

Snippet of the CHARM hierarchical data table

Part of the CHARM ROI organizational table text file included in NMT download


Example images

The following images were made using the symmetric NMT v2 template (with “standard” spatial resolution = 0.25 mm, and FOV = brain volume) and accompanying CHARM.

Skull-stripped NMT with the CHARM (level 1)


Skull-stripped NMT with the CHARM (level 2)


Skull-stripped NMT with the CHARM (level 3)


Skull-stripped NMT with the CHARM (level 4)


Skull-stripped NMT with the CHARM (level 5)


Skull-stripped NMT with the CHARM (level 6)


The script used to make these images with ``@chauffeur_afni`` is available here: do_view_charm.tcsh.


The CHARM is distributed as part of the NMT v2 download. For each form/variant of the NMT, there is a matching CHARM dataset, as well.

To download and unpack the datasets, please see the instructions...


If you make use of the CHARM and/or accompanying NMT v2 data in your research, please cite:

Jung, B., Taylor, P.A., Seidlitz, J., Sponheim, C., Perkins P., Ungerleider, L.G., Glen, D., Messinger, A. (2021) “A comprehensive macaque fMRI pipeline and hierarchical atlas.” NeuroImage, submitted.
Reveley C, Gruslys A, Ye FQ, Glen D, Samaha J, E Russ B, Saad Z, K Seth A, Leopold DA, Saleem KS (2017). Three-Dimensional Digital Template Atlas of the Macaque Brain. Cereb Cortex 27(9):4463-4477. doi: 10.1093/cercor/bhw248.
For questions, comments and/or suggestions, contact:
Adam.Messinger @ nih.gov
benjamin.jung @ nih.gov
glend @ mail.nih.gov.