DOI: 10.5281/zenodo.17258389
title: CMIG Atlases

description: Overview 

The ABCD atlas was synthesized using the Multimodal Image Normalisation Tool (MINT) developed by the Data, Analysis and Informatics Resource Center of the ABCD study using adolescent brain MRI data from the ABCD Study®. The MINT ABCD atlas is generated from 1000 observations from baseline and two-year follow up imaging data. Below is a brief overview, for more details please see Pecheva et al. (2022).

Intended use 

The ABCD atlas was created to facilitate analyses of multimodal MRI data using the statistical package FEMA (Parekh et al., 2024). All available scans from all observations included in ABCD Data Release 6.0 were registered to the ABCD atlas. For details on how to use the ABCD atlas along with ABCD Release 6.0 data for whole-brain voxelwise linear mixed effects analyses in FEMA, please see the description of the ABCD concatenated data and the FEMA package. 

What’s included

These sections provide overviews of the contents of each .zip file. Please see the detailed file descriptions for more information. Data are provided as .mat and NIfTI files where possible.

ABCD3_cor10

The ABCD atlas includes group representative volumes of the following modalities:





T1w




T2w




Spherical harmonics coefficients derived using the restricted sprectrum imaging (RSI) model for three compartments: restricted, hindered and free water




RGB colour-coded FA map




Anatomical labels of 






cortical and subcortical structures from Freesurfer’s Deskian/Killiany parcellation (Desikan et al., Neuroimage, 2006) 




white matter tract parcellation from AltasTrack (Hagler et al., Hum. Brain Mapp., 2009).




abcd3_rel6.0

In addition to these atlas files, all available scans from all observations included in Data Release 6.0 of the ABCD study were registered to the ABCD atlas. Participants' cortical, subcortical and white matter parcellations were warped to atlas space and averaged to create probabilistic anatomical labels of cortical, subcortical and white matter structures specific to the ABCD Release 6.0 data. These probabilistic labels differ from the labels in ABCD3_cor10 only in the observations included in generating them. 

external_parcellations

We incorporated two independent brain parcellations into the MINT ABCD space to provide parcellations of subcortical structures not available from Freesurfer or AtlasTrack:





Subcortical atlas that was generated using T1 and T2 scans from 168 typical adults from the Human Connectome Project (HCP) (Pauli et al., 2018), 




Thalamic nuclei atlas that was generated from adult HCP data from 70 participants (Najdenovska et al., 2018).



showVolData

Here are included atlas files in the formats required by the MATLAB-based MR volume viewer distributed as part of the FEMA package. 

Atlas creation 

Images were registered using rigid body, affine and nonlinear transformations. In total eleven multimodal channels were used to align scans and create the MINT ABCD atlas, however the input channels varied according to the registration step. Three structural MRI (sMRI) channels were included: T1w images, white matter segmentation, and grey matter segmentation; and eight diffusion MRI (dMRI) channels: the zeroth and second order spherical harmonics (SH) coefficients of the restricted orientation distribution function (ODF) and the zeroth order SH coefficients from the hindered and free water ODFs from the restriction spectrum imaging (RSI) model. sMRI and dMRI channels were first aligned within-subject using rigid body registration transforms. Then inter-subject anatomical alignment was achieved using rigid body, affine and nonlinear transforms. A group average was computed for each channel across the 1000 scans best aligned with the registration target, based on the mean Pearson correlation across all eleven input channels. The registration target was updated with the new multimodal average and the procedure was repeated three times, producing the iteratively refined multimodal ABCD atlas. 

References 

Pecheva, D., Iversen, J. R., Palmer, C. E., Watts, R., Jernigan, T. L., Hagler, D. J., & Dale, A. M. (2022). Multimodal Image Normalisation Tool (MINT) for the Adolescent Brain and Cognitive Development study: The MINT ABCD Atlas. bioRxiv. https://doi.org/10.1101/2022.08.09.503395 

Parekh, P., Fan, C. C., Frei, O., Palmer, C. E., Smith, D. M., Makowski, C., Iversen, J. R., Pecheva, D., Holland, D., Loughnan, R., Nedelec, P., Thompson, W. K., Hagler, D. J. Jr, Andreassen, O. A., Jernigan, T. L., Nichols, T. E., & Dale, A. M. (2024). FEMA: Fast and efficient mixed-effects algorithm for large sample whole-brain imaging data. Human Brain Mapping, 45(2), e26579. https://doi.org/10.1002/hbm.26579 

Najdenovska, E., Alemán-Gómez, Y., Battistella, G., Descoteaux, M., Hagmann, P., Jacquemont, S., Maeder, P., Thiran, J.-P., Fornari, E., & Bach Cuadra, M. (2018). Scientific Data, 5(1), 180270. https://doi.org/10.1038/sdata.2018.270 

Pauli, W. M., Nili, A. N., & Tyszka, J. M. (2018). Scientific Data, 5(1), 180063. https://doi.org/10.1038/sdata.2018.63 
description: File descrtiptions




Folder
File name
Description


ABCD3_cor10
ABCD3_cor10_CO_FA.nii.gz




RGB volume of color-coded FA map




ABCD3_cor10
ABCD3_cor10_RND.nii.gz




Restricted normalised directional map




ABCD3_cor10
ABCD3_cor10_T1.nii.gz




ABCD3 atlas T1w volume




ABCD3_cor10
ABCD3_cor10_T2.nii.gz




ABCD3 atlas T2w volume




ABCD3_cor10
ABCD3_cor10_aparcaseg_rois.nii.gz




4D volume of ABCD3 atlas ROIs derived from FreeSurfer cortical parcellation (aparc) and subcortical segmentation (aseg) data




ABCD3_cor10
ABCD3_cor10_aparcaseg_rbg.nii.gz




RGB volume of ABCD3 atlas ROIs derived from FreeSurfer cortical parcellation (aparc) and subcortical segmentation (aseg) data




ABCD3_cor10
ABCD3_cor10_aseg_rois.nii.gz




4D volume of ABCD3 atlas ROIs from the Freesurfer automatic subcortical segmentation (aseg)




ABCD3_cor10
ABCD3_cor10_aseg_rbg.nii.gz




4D volume of ABCD3 atlas ROIs derived from FreeSurfer subcortical segmentation (aseg) data




ABCD3_cor10
ABCD3_cor10_fiber_rois.nii.gz




4D volume of ABCD3 atlas ROIs derived from AtlasTrack labels of white matter tracts




ABCD3_cor10
ABCD3_cor10_fiber_rbg.nii.gz




RGB volume of ABCD3 atlas ROIs derived from AtlasTrack labels of white matter tracts




ABCD3_cor10
ABCD3_cor10_gm_new_seg.nii.gz




ABCD3 cortical grey matter ROI (including cerebellum)




ABCD3_cor10
ABCD3_cor10_wm_seg.nii.gz




ABCD3 white matter ROI




ABCD3_cor10
ABCD3_cor10_seg.nii.gz




Combined grey and white matter parcellations




ABCD3_cor10
atlas_dspace_ABCD3_cor10.mat




Complete ABCD3 atlas volumes, see "Matlab files" section for details




abcd_rel6.0
aparcaseg.mat




Probabilistic ROIs from the ABCD Study Release 6.0, derived from FreeSurfer cortical parcellation (aparc) and subcortical segmentation (aseg) data




abcd_rel6.0
aparcaseg_rois.nii.gz




4D volume of probabilistic ROIs from the ABCD Study Release 6.0, derived from FreeSurfer cortical parcellation (aparc) and subcortical segmentation (aseg) data




abcd_rel6.0
aparcaseg_rgb.nii.gz




RGB volume of probabilistic ROIs from the ABCD Study Release 6.0, derived from FreeSurfer cortical parcellation (aparc) and subcortical segmentation (aseg) data




abcd_rel6.0
aseg.mat




Probabilistic ROIs from the ABCD Study Release 6.0, derived from FreeSurfer subcortical segmentation (aseg) data




abcd_rel6.0
aseg_rois.nii.gz




4D volume of probabilistic ROIs from the ABCD Study Release 6.0, derived from FreeSurfer subcortical segmentation (aseg) data




abcd_rel6.0
aseg_rgb.nii.gz




RGB volume of probabilistic ROIs from the ABCD Study Release 6.0, derived from FreeSurfer subcortical segmentation (aseg) data




abcd_rel6.0
fiber.mat




Probabilistic ROIs from the ABCD Study Release 6.0, derived from AtlasTrack labels of white matter tracts




abcd_rel6.0
fiber_rois.nii.gz




4D volume of probabilistic ROIs from the ABCD Study Release 6.0, derived from AtlasTrack labels of white matter tracts




abcd_rel6.0
fiber_rgb.nii.gz




RGB volume of probabilistic ROIs from the ABCD Study Release 6.0, derived from AtlasTrack labels of white matter tracts




external_parcellations
pauli_subcortnuclei_abcd3_cor10.mat




Subcortical ROIs from Pauli et al. warped to ABCD3 atlas space (Pauli, W. M., Nili, A. N., & Tyszka, J. M. (2018). Scientific Data, 5(1), 180063. https://doi.org/10.1038/sdata2018.63 )




external_parcellations
pauli_subcortnuclei_abcd3_cor10_rois.nii.gz




4D volume of the subcortical ROIs from Pauli et al. in ABCD3 atlas space




external_parcellations
pauli_subcortnuclei_abcd3_cor10_rgb.nii.gz




RGB volume of the subcortical ROIs from Pauli et al. in ABCD3 atlas space




external_parcellations
pauli_subcortnuclei_lut.csv




Look up table for the subcortical ROIs laballed in Pauli et al.




external_parcellations
thalamus_abcd3_cor10.mat




Thalamic nuclei ROIs from Najdenovska et al. warped to ABCD3 atlas space (Najdenovska, E., Alemán-Gómez, Y., Battistella, G., Descoteaux, M., Hagmann, P., Jacquemont, S., Maeder, P., Thiran, J.-P., Fornari, E., & Bach Cuadra, M. (2018). Scientific Data, 5(1), 180270. https://doi.org/10.1038/sdata2018.270)




external_parcellations
thalamus_abcd3_cor10_rois.nii.gz




4D volume of the thalamic nuclei ROIs from Najdenovska et al. in ABCD3 atlas space




external_parcellations
thalamus_abcd3_cor10_rgb.nii.gz




RGB volume of the thalamic nuclei ROIs from Najdenovska et al. in ABCD3 atlas space




external_parcellations
thalamus_lut.csv




Look up table for the thalamic ROIs laballed in Najdenovska et al.




showVolData
aparcaseg_rgb_6.0_ABCD3_cor10.mat




Probabilistic aparc+aseg RGB ROIs from the ABCD Study Release 6.0




showVolData
aseg_rgb_6.0_ABCD3_cor10.mat




Probabilistic aseg RGB ROIs from the ABCD Study Release 6.0




showVolData
CO_6.0_ABCD3_cor10.mat




RGB volume of color-coded FA map of the ABCD3 atlas




showVolData
fiber_rgb_6.0_ABCD3_cor10.mat




Probabilistic white matter fiber RGB ROIs from the ABCD Study Release 6.0




showVolData
pauli_rgb_6.0_ABCD3_cor10.mat




Subcortical RGB ROIs from Pauli et al.




showVolData
pauli_rgb_T1_6.0_ABCD3_cor10.mat




Subcortical RGB ROIs from Pauli et al. overlaid on the Pauli atlas T1 image, in ABCD3 space




showVolData
pauli_T1_6.0_ABCD3_cor10.mat




Pauli atlas T1 image, in ABCD3 space




showVolData
pauli_T2_6.0_ABCD3_cor10.mat




Pauli atlas T2 image, in ABCD3 space




showVolData
showVolAtlases_6.0_ABCD3_cor10.mat




Combined data from all atlas listed in this directory




showVolData
T1_6.0_ABCD3_cor10.mat




ABCD3 atlas T1w volume




showVolData
T2_6.0_ABCD3_cor10.mat




ABCD3 atlas T2w volume




showVolData
thalamus_rgb_6.0_ABCD3_cor10.mat




Thalamic nuclei RGB ROIs from Najdenovska et al.




showVolData
thalamus_rgb_T1_6.0_ABCD3_cor10.mat




Thamalic nuclei RGB ROIs from Najdenovska et al. overlaid on the Najdenovska atlas T1 image, in ABCD3 space




showVolData
thalamus_T1_6.0_ABCD3_cor10.mat




Najdenovska atlas T1 image, in ABCD3 space
description: Matlab files contents

Some Matlab files contain multple variables, those that do are decribed below.         

ABCD3_cor10 

 atlas_dspace_ABCD3_cor10.mat




Variable name
Description


M_atl
Affine transform of ABCD3 atlas


surfstructs_reg_mu
N/A


muvertcoords_af
N/A


muvertcoords_reg
N/A


muvols_nz
N/A


agelist
N/A


sexlist
N/A


muvols_T2
ABCD3 atlas average T2w volume


stdvols_T2




Standard deviation of the T2w volumes included in the ABCD3 atlas




muvols_T1_af




ABCD3 atlas average T1w volume after only affine registration




stdvols_T1_af




Standard deviation of the T1w volumes included in the ABCD3 atlas




muvols_T1
ABCD3 atlas average T1w volume


stdvols_T1




Standard deviation of the T1w volumes included in the ABCD3 atlas




muvols_b0




ABCD3 atlas average dMRI b=0mm/s2 volume




stdvols_b0




Standard deviation of the b=0mm/s2 volumes included in the ABCD3 atlas




muvols
ABCD3 atlas average of DTI eigenvectors


stdvols




Standard deviation io the DTI eigenvectors volumes included in the ABCD3 atlas




muvols_MF




ABCD atlas average spherical harmonics coefficients derived using the restricted sprectrum imaging (RSI) model for three compartments: restricted=columns 1-15; hindered=columns16-30; free water=column 31




stdvols_MF




Standard deviation of the spherical harmonics coeffiecient volumes included in the ABCD3 atlas




muvols_bm




ABCD3 atlas average of smoothed, filled-in brain masks derived from nonzero voxels of the FreeSurfer wmparc segmentation




muvols_wm
ABCD3 white matter ROI


muvols_gm




ABCD3 atlas cortical grey matter ROI (excluding cerebellum)




muvols_gm_new




ABCD3 atlas cortical grey matter ROI (including cerebellum)




muvols_lv
ABCD3 atlas ventricles ROI


indlist_fiber




Codes for ROIs derived from AtlasTrack labels of white matter tracts




filist_fiber




Entire potential label numeric code range for the AltasTrack segmentation data




indlist_aseg




Numeric codes for ROIs derived from FreeSurfer subcortical segmentation (aseg) data




filist_aseg




Entire potential label numeric code range for the aseg segmentation data




indlist_aparcaseg




Numeric codes for ROIs derived from FreeSurfer cortical parcellation (aparc) and subcortical segmentation (aseg) data




filist_aparcaseg




Entire potential label numeric code range for the aparcaseg segmentation data




indlist_wmparc




Numeric codes for ROIs derived from FreeSurfer white matter parcellation (wmparc)




filist_wmparc




Entire potential label numeric code range for the wmparc segmentation data




muvols_fiber




ABCD3 atlas ROIs derived from AtlasTrack labels of white matter tracts




muvols_aseg




ABCD3 atlas ROIs derived from FreeSurfer subcortical segmentation (aseg) data




muvols_aparcaseg




ABCD3 atlas ROIs derived from FreeSurfer cortical parcellation (aparc) and subcortical segmentation (aseg) data




muvols_wmparc




ABCD3 atlas ROIs derived from FreeSurfer white matter parcellation (wmparc)




vol_mask_aseg




ABCD3 atlas smoothed whole-brain mask derived from muvols_wmparc voxels>0.5




vol_CO_rgb
RGB volume of color-coded FA map




 

abcd3_rel6.0 

aparcaseg.mat, aseg.mat, fiber.mat 




Variable name
Description


volmat_prob




matrix of size X x Y x Z x R where X,Y,Z voxels dimension and R is number of ROIs




volmat_prob_rgb




5D matrix of size X x Y x Z x R x 3 where X,Y,Z voxels dimension and R is number of ROIs




volmat_prob_rgbsum




4D matrix of size X x Y x Z x 3 where X,Y,Z voxels dimensions




roicodes
array of ROI numeric identifiers


roinames
ROI names


roirgb
ROI RGB color codes




 

external_parcellations

pauli_subcortnuclei_abcd3_cor10.mat




Variable name
Description


D_fwd




combined 3D nonlinear warp from subcortical nuclei atlas to ABCD atlas




M_atl
Affine transform of ABCD3 atlas


M_reg_af




reslice matrix from ABCD atlas to subcortical nuclei atlas




di1vol1
nonlinear deformation field for y-direction


di2vol1
nonlinear deformation field for x-direction


di3vol1
nonlinear deformation field for z-direction


muvols_T1_ctx
ABCD atlas T1 volume


pauli_lut




look up table for ROI code, name and RGB color code




vol_T1




subcortical nuclei atlas T1 volume in original space




vol_T1_af




subcortical nuclei atlas T1 volume affine transformed to ABCD atlas space




vol_T1_rb




subcortical nuclei atlas T1 volume rigid body transformed to ABCD atlas space




vol_T1_reg




subcortical nuclei atlas T1 volume nonlinearly transformed to ABCD atlas space




vol_T2




subcortical nuclei atlas T2 volume in original space




vol_T2_af




subcortical nuclei atlas T2 volume affine transformed to ABCD atlas space




vol_T2_rb




subcortical nuclei atlas T2 volume rigid body transformed to ABCD atlas space




vol_T2_reg




subcortical nuclei atlas T2 volume nonlinearly transformed to ABCD atlas space




vol_labels_T1_reg_rgb




color coded segmentation volume nonlinearly transformed to ABCD atlas space




vol_labels_af




segmentation volume affine transformed to ABCD atlas space




vol_labels_reg




segmentation volume rigid body transformed to ABCD atlas space




vol_labels_reg_rgb




segmentation volume nonlinearly transformed to ABCD atlas space




vol_labels_res_T1




segmentation volume in original space, T1 resolution




volresfun_reg




function handle to transform subcortical nuclei atlas to ABCD atlas space






 

thalamus_abcd3_cor10.mat    




Variable name
Description


D_fwd




combined 3D nonlinear warp from thalamic nuclei atlas to ABCD atlas




M_atl
Affine transform of ABCD3 atlas


M_reg_af




reslice matrix from ABCD atlas to thalamic nuclei atlas




di1vol1
nonlinear deformation field for y-direction


di2vol1
nonlinear deformation field for x-direction


di3vol1
nonlinear deformation field for z-direction


muvols_T1_ctx
ABCD atlas T1 volume


thalamus_lut




look up table for ROI code, name and RGB color code




vol_T1




thalamic nuclei atlas T1 volume in original space




vol_T1_af




thalamic nuclei atlas T1 volume affine transformed to ABCD atlas space




vol_T1_rb




thalamic nuclei atlas T1 volume rigid body transformed to ABCD atlas space




vol_T1_reg




thalamic nuclei atlas T1 volume nonlinearly transformed to ABCD atlas space




vol_labels_T1_reg_rgb




color coded T1 volume nonlinearly transformed to ABCD atlas space




vol_labels_af




segmentation volume affine transformed to ABCD atlas space




vol_labels_reg




segmentation volume nonlinearly transformed to ABCD atlas space




vol_labels_reg_rgb




color coded segmentation volume nonlinearly transformed to ABCD atlas space




vol_labels_res_T1




segmentation volume in original space, T1 resolution




volresfun_reg




function handle to transform thalamic atlas to ABCD atlas space