Parcellations and Methodologies

This section describes all available parcellations for each supra-region in CHIMERA.

Overview

CHIMERA defines ten different supra-regions where each can be parcellated using different methodologies. The parcellation code consists of 10 characters, one for each supra-region, allowing you to create custom combinations.

Available Parcellations by Supra-region

1. Cortical (Supra-region: Cortical)

The first character of the parcellation code selects the cortical parcellation method.

Code	Name	Citation	Code	Name	Citation
A	AALv2	Rolls et al, 2015	B	Brainnetome	Fan et al, 2016
C	Campbell	Campbell, 1905	D	Desikan-Killiany	Desikan et al, 2006
F	Flechsig	Flechsig, 1920	H	HCP-MMP1	Glasser et al, 2016
K	Kleist	Kleist, 1934	L	Lausanne	Symmetric version of Cammoun et al, 2012
M	Smith	Smith et al, 1907	R	Broadmann	Broadmann, 1909
S	Schaefer	Schaefer et al, 2018	T	Desikan-Killiany-Tourville	Klein and Tourville, 2012
V	vonEconomo	von Economo and Koskinas, 1925	X	Destrieux	Destrieux et al, 2009
Y	Yeo	Yeo et al, 2011

2. Subcortical (Supra-region: Subcortical)

The second character selects the subcortical structures parcellation method.

Code	Name	Citation
F	Aseg	Fischl et al, 2002
R	FIRST	Patenaude et al, 2011

3. Thalamus (Supra-region: Thalamus)

The third character selects the thalamic parcellation method.

Code	Name	Citation	Code	Name	Citation
F	Aseg	Fischl et al, 2002	I	FSThalParc	Iglesias et al, 2018
M	MIALThalParc	Najdenovska and Aleman-Gomez et al, 2018	R	FIRST	Patenaude et al, 2011

4. Amygdala (Supra-region: Amygdala)

The fourth character selects the amygdala parcellation method.

Code	Name	Citation
F	Aseg	Fischl et al, 2002
I	FSAmygHippoParc	Saygin et al, 2017
R	FIRST	Patenaude et al, 2011

5. Hippocampus (Supra-region: Hippocampus)

The fifth character selects the hippocampal parcellation method.

Code	Name	Citation	Code	Name	Citation
F	Aseg	Fischl et al, 2002	I	FSAmygHippoParc	Iglesias et al, 2015
H	HBT	Iglesias et al, 2015	R	FIRST	Patenaude et al, 2011

6. Hypothalamus (Supra-region: Hypothalamus)

The sixth character selects the hypothalamic parcellation method.

Code	Name	Citation
F	Aseg	Based on in-house protocol
I	FSHypoThalParc	Billot et al, 2020

7. Cerebellum (Supra-region: Cerebellum)

The seventh character selects the cerebellar parcellation method.

Code	Name	Citation
A	AALv2	Rolls et al, 2015
F	Aseg	Fischl et al, 2002
S	SUIT	Diedrichsen, J. et al, 2009

8. Brainstem (Supra-region: Brainstem)

The eighth character selects the brainstem parcellation method.

Code	Name	Citation
F	Aseg	Fischl et al, 2002
I	FSBrainStemParc	Iglesias et al, 2015
R	FIRST	Patenaude et al, 2011

9. Gyral White Matter (Supra-region: GyralWM)

The ninth character selects the gyral white matter parcellation method.

Code	Name	Citation
F	Cortical	Depends on the cortical parcellation

10. White Matter (Supra-region: WhiteMatter)

The tenth character selects the white matter parcellation method.

Code	Name	Citation
F	Aseg	Fischl et al, 2002
J	JHU	Hua et al, 2008

Example Parcellation Codes

Here are some example codes and their meanings:

LFMIIIFIF (Recommended default):

L: Lausanne multiscale cortical parcellation
F: FreeSurfer subcortical structures
M: MIAL thalamic nuclei
I: FreeSurfer amygdala nuclei
I: FreeSurfer hippocampal subfields
I: FreeSurfer hypothalamic regions
S: SUIT parcellation for the cerebellum
I: FreeSurfer brainstem regions
F: Cortical-based gyral white matter
F: FreeSurfer white matter

HFIIIIFIF (High-resolution cortical):

H: HCP-MMP1 high-resolution cortical (360 regions)
F: FreeSurfer subcortical structures
I: FreeSurfer thalamic nuclei
(rest same as above)

SFMIIIFIF (Schaefer cortical):

S: Schaefer cortical parcellation (customizable scale)
F: FreeSurfer subcortical structures
M: MIAL thalamic nuclei
(rest same as above)

Command Line Usage

To see all available parcellations:

chimera --regions

To use a specific parcellation code:

chimera -b /path/to/bids -d /path/to/derivatives -p DFMIIIFIF