Neurodevelopmental MRI Database

About

This is a database of average MRIs and associated MRI volumes for developmental MRI work. It consists of average MRI templates, segmented partial volume estimate volumes for GM, WM, T2W-derived CSF. The database is separated into head-based and brain-based averages. The data are separated by ages in months, years, 6-month, or 5-year intervals. The templates are grouped into first year (2 weeks through 12 months), early childhood (15 months through 4 years), childhood (4 years through 10 years), adolescence (10.5 years through 17.5 years) and adults (18 years through 89 years).

Tools for cortical source analysis of EEG and ERP are provided. These tools are based on the average MRI templates, segmenting, and atlases.

Terms of use: The MRI templates from this database are freely available and distributed for scientific work. The CC BY-NC-ND 3.0 license allows sharing but users should inform JER of any sharing. These should not be modified or used in commercial applications. Publications from this work should cite the publications for the data upon which these templates are based. JER retains all copyrights to the templates.

Creative Commons License
Neurodevelopmental MRI Database by John E. Richards is licensed under a Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported License.

Contact John E. Richards (richards-john@sc.edu) for access to the volumes.

Citations

Publications from this work should cite the publications for the data upon which these templates are based.

For the infants and preschool (0 to 4 years), please cite publications from the NIH Pediatric MRI Database (NIHPD; Almli, C. R., Rivkin, M. J., & McKinstry, R. C. (2007). The NIH MRI study of normal brain development (objective-2): Newborns, infants, toddlers, and preschoolers. Neuroimage, 35(1), 308-325), and from Sanchez, C.E., Richards, J.E., & Almli, C.R. (2011). Neurodevelopmental MRI brain templates for children from 2 weeks to 4 years of age, Developmental Psychobiology Online PDF; Richards, J.E. (2009).
Attention in the brain and early infancy. In S.P. Johnson (Ed.), Neoconstructism: The new science of cognitive development Online PDF; Richards, J.E. (2010). What’s inside a baby’s head? Structural and functional brain development in infants. International Conference on Infant Studies, Baltimore, MD, March, 2010.Online PDF; Richards, J.E., & Xie, W. (2015). Brains for all the ages: Structural neurodevelopment in infants and children from a life-span perspective. In J. Bensen (Ed.), Advances in Child Development and Behavior (Vol 48, Chapter 1, pps 1-52).; Richards, J.E., Sanchez, C., Phillips-Meek, M., & Xie, W. (2015). A database of age-appropriate average MRI templates, Neuroimage, doi:10.1016/j.neuroimage.2015.04.055; Fillmore, P.T., Richards, J.E., Phillips-Meek, M.C., Cryer, A., & Stevens, M. (2015). Stereotaxic MRI brain atlases for infants from 3 to 12 months of age. Developmental Neuroscience, doi:10.1156/000438749.

For the children and adolescents, please cite publications from the NIHPD (Evans, A. C. (2006). The NIH MRI study of normal brain development. Neuroimage, 30(1), 184-202.); Sanchez, C.E., Richards, J.E., & Almli, C.R. (2010). Age-specific MRI brain templates for healthy brain development from 4 to 24 years, Unpublished ms.; Sanchez, C.E., Richards, J.E., & Almli, C.R. (2012). Age-specific MRI templates for pediatric neuroimaging. Developmental Neuropsychology, 37, 379-399. Online PDF; and Richards, J.E., & Xie, W. (2015). Brains for all the ages: Structural neurodevelopment in infants and children from a life-span perspective. In J. Bensen (Ed.), Advances in Child Development and Behavior (Vol 48, Chapter 1, pps 1-52); Richards, J.E., Sanchez, C., Phillips-Meek, M., & Xie, W. (2015). A database of age-appropriate average MRI templates. Neuroimage, doi:10.1016/j.neuroimage.2015.04.055.

For the adults, please cite Sanchez, C.E., Richards, J.E., & Almli, C.R. (2012). Age-specific MRI templates for pediatric neuroimaging. Developmental Neuropsychology, 37, 379-399, Online PDF. Fillmore, P.T., Phillips-Meek, M.C., and Richards, J.E. (2013), Age-specific MRI brain and head templates for healthy adults from 20 through 89 years of age. Frontiers in Aging Neuroscience.6, doi: 10.3389/fnagi.2015.00044; Richards, J.E., & Xie, W. (2015). Brains for all the ages: Structural neurodevelopment in infants and children from a life-span perspective. In J. Bensen (Ed.), Advances in Child Development and Behavior (Vol 48, Chapter 1, pps 1-52); Richards, J.E., Sanchez, C., Phillips-Meek, M., & Xie, W. (2015). A database of age-appropriate average MRI templates. Neuroimage, doi:10.1016/j.neuroimage.2015.04.055. and work from the IXF and OASIS MRI projects

There are two recent publications that summarize much of the work: Richards, J.E., & Xie, W. (2015). Brains for all the ages: Structural neurodevelopment in infants and children from a life-span perspective. In J. Bensen (Ed.), Advances in Child Development and Behavior (Vol 48, Chapter 1, pps 1-52; Richards, J.E., Sanchez, C., Phillips-Meek, M., & Xie, W. (2015). A database of age-appropriate average MRI templates. Neuroimage,doi:10.1016/j.neuroimage.2015.04.055.

Description


The database consists of MRI average templates for a number of ages; in 1-3 month increments through 18 months; then half-year increments through 19-5 years; then 5 year increments through 89 years. The templates were done separately for brain and head. Also included are segmentation PVE volumes for gm/wm/csf; T2W-derived CSF; and non-myelinated axons (NMA) for infants. Access to the dataset is separated by ages (infants; 0-12 mo; preschool, 15 mo through 4-0 years; children 4-5 through 10-5 yrs; adolescents 11-0 through 17-5 yrs; adults 20-89 years).

The segment data for ages 15-months and older consists of GM, WM, CSF, and T2W-derived CSF. The best combination of segments would be the image_aposteriori_seg data, using GM, WM, and T2W-derived CSF for priors. For 3 through 12 months, the best combination of segments would be the nma_seg data; using GM, WM, NMA, and T2W-derived CSF. The “CSF” PVE segments are “Other Matter” in a 3-class segmentation (GM, WM, “Other Matter”) and does not reflect actual CSF. The T2W-derived CSF is identified as bright voxels in the T2W scan and represent actual CSF in the brain or head. There is an atlas derived from FSL “Harvard-Oxford” cortical and subcortical atlas for the infants, 8 10 12 14 16 18, and 20-24 year old templates.

Overview:
ANTS….brain.nii.gz: Average MRI template derived from extracted brain
ANTS….head.nii.gz: Average MRI template derived from whole head
ANTS….brain-head: brain extracted from head template
ANTS….T2W_brain: MRI template separate for extracted brain T2W
ANTS….T2W_head: MRI template separate for whole head T2W

Segments
AVG…T2W_brain…: T2W for individual participants, warped to template, averaged
AVG…image_seg_…: Image-based segment averages
AVG…image_aposteriori_seg_.. : Age-template priors with a posteriori FAST
AVG…MNI_aposteriori_seg_…: AVG of MNI-template priors, with a posteriori FAST
AVG…nma_seg_: For infants, non-myelinated axons separate from gray matter
AVG….seg_csf: “Other matter” in 3-class segmentation
AVG….seg_t2wcsf: T2W-derived CSF

Atlas:
ANTS…brain…brainstem: The individual files have the brain areas
ANTS…brain_atlas: Segmented atlas for all brain areas

Ages and Templates


Infants

 
Age 1.5T 3.0T Total Notes
2-0Weeks 23 23
3-0Months 22 14 36 Separate 3-0T, NMA, Atlas, Participant Source Model (3-0T), Average Source Model (1-5T, 3-0T)
4-5Months N/A 12/13 12 3-0T only, NMA, Atlas, Participant Source Model (3-0T), Average Source Model (1-5T, 3-0T)   Version1/Version2
6-0Months 32 14/76 46 Separate 3-0T, Atlas, Participant Source Model (3-0T), Average Source Model (3-0T); Total is 1.5+Version1-3.0T avg; Version1/Version2
7-5Months N/A 11/61 11 3-0T only, NMA, Atlas, Participant Source Model (3-0T), Average Source Model (1-5T, 3-0T) Version1/Version2
9-0Months 29 10/12 34 Separate 3-0T, Atlas, Participant Source Model (3-0T), Average Source Model (3-0T); Total is 1.5+Version1-3.0T avg; Version1/Version2
10-5Months N/A 2 N/A 3-0T only, NMA, Atlas, Participant Source Model (3-0T), Average Source Model (1-5T, 3-0T)
12-0Months 25 12/105 35 Separate 3-0T, Atlas, Participant Source Model (3-0T), Average Source Model (3-0T); Total is 1.5+Version1-3.0T avg; Version1/Version2

Preschool

Age 1.5T 3.0T Total Notes
15-0 Months 32 32 1-5T only, Average Source Model
18-0 Months 32 0/40 32
Separate 3-0T, Atlas, Participant Source Model (3-0T), Average Source Model (3-0T); Total is 1.5 Version 1 only; Version1/Version2
2-0 Years 27 73 27 Separate 3-0T, Atlas, Participant Source Model (3-0T), Average Source Model (3-0T); Total is 1.5 only
2-5 Years 31 31 1-5T only, Average Source Model
3-0 Years 22 24 22 Separate 3-0T, Atlas, Participant Source Model (3-0T), Average Source Model (3-0T); Total is 1.5 only
4-0 Years 19 10 / 24 19 Separate 3-0T, Atlas, Participant Source Model (3-0T), Average Source Model (3-0T); Total is 1.5+Version1-3.0T avg; Version1/Version2

Children

 
Age 1.5T 3.0T Total Notes
4-5 Years 9 18 9 Separate 3-0T, Atlas, Participant Source Model (3-0T), Average Source Model (3-0T); Total is 1.5 only
5-0 Years 14 29 14 Separate 3-0T, Atlas, Participant Source Model (3-0T), Average Source Model (3-0T); Total is 1.5 only
5-5 Years 17 29 17 Separate 3-0T, Atlas, Participant Source Model (3-0T), Average Source Model (3-0T); Total is 1.5 only
6-0 Years 27 10 / 45 37 Separate 3-0T, Atlas, Participant Source Model (3-0T), Average Source Model (3-0T); Total is 1.5+Version1-3.0T avg; Version1/Version2
6-5 Years 36 33 36 Separate 3-0T, Atlas, Participant Source Model (3-0T), Average Source Model (3-0T); Total is 1.5 only
7-0 Years 27 39 27  Separate 3-0T, Atlas, Participant Source Model (3-0T), Average Source Model (3-0T); Total is 1.5 only
7-5 Years 44 37 44 Separate 3-0T, Atlas, Participant Source Model (3-0T), Average Source Model (3-0T); Total is 1.5 only
8-0 Years 46 19 / 82 56 Separate 3-0T, Atlas, Participant Source Model (3-0T), Average Source Model (3-0T); Total is 1.5+Version1-3.0T avg; Version1/Version2
8-5 Years 40 12 /110 40 Separate 3-0T, Atlas, Participant Source Model (3-0T), Average Source Model (3-0T); Total is 1.5+Version1-3.0T avg; Version1/Version2
9-0 Years 46 95 46 Separate 3-0T, Atlas, Participant Source Model (3-0T), Average Source Model (3-0T); Total is 1.5 only
9-5 Years 41 10 / 102 41 Separate 3-0T, Atlas, Participant Source Model (3-0T), Average Source Model (3-0T); Total is 1.5+Version1-3.0T avg; Version1/Version2
10-0 Years 62 16 / 104 72 Separate 3-0T, Atlas, Participant Source Model (3-0T), Average Source Model (3-0T); Total is 1.5+Version1-3.0T avg; Version1/Version2
10-5 Years 52 93 52 Separate 3-0T, Atlas, Participant Source Model (3-0T), Average Source Model (3-0T); Total is 1.5 only

Adolescents

 
Age 1.5T 3.0T Total Notes
11-0 Years 31 84 31 *Version2 will have Separate 3-0T, Atlas, Participant Source Model (3-0T), Average Source Model (3-0T); Total is 1.5 only
11-5 Years 40 90 40 *Version2 will have Separate 3-0T, Atlas, Participant Source Model (3-0T), Average Source Model (3-0T); Total is 1.5 only
12-0 Years 37 15 / 106 47 Separate 3-0T, Atlas, Participant Source Model (3-0T), Average Source Model (3-0T); Total is 1.5+Version1-3.0T avg; Version1/Version2
12-5 Years 30 122 30 *Version2 will have Separate 3-0T, Atlas, Participant Source Model (3-0T), Average Source Model (3-0T); Total is 1.5 only
13-0 Years 34 11 / 105 34 *Version2 will have Separate 3-0T, Atlas, Participant Source Model (3-0T), Average Source Model (3-0T); Total is 1.5 only
13-5 Years 29 19 / 136 29 *Version2 will have Separate 3-0T, Atlas, Participant Source Model (3-0T), Average Source Model (3-0T); Total is 1.5 only
14-0 Years 32 30 / 127 42 Separate 3-0T, Atlas, Participant Source Model (3-0T), Average Source Model (3-0T); Total is 1.5+Version1-3.0T avg; Version1/Version2
14-5 Years 30 85 31 *Version2 will have Separate 3-0T, Atlas, Participant Source Model (3-0T), Average Source Model (3-0T); Total is 1.5 only
15-0 Years 32 100 32 *Version2 will have Separate 3-0T, Atlas, Participant Source Model (3-0T), Average Source Model (3-0T); Total is 1.5 only
15-5 Years 23 98 23 *Version2 will have Separate 3-0T, Atlas, Participant Source Model (3-0T), Average Source Model (3-0T); Total is 1.5 only
16-0 Years 34 13 / 98 44 Separate 3-0T, Atlas, Participant Source Model (3-0T), Average Source Model (3-0T); Total is 1.5+Version1-3.0T avg; Version1/Version2
16-5 Years 28 95 29 *Version2 will have Separate 3-0T, Atlas, Participant Source Model (3-0T), Average Source Model (3-0T); Total is 1.5 only
17-0 Years 25 87 25 *Version2 will have Separate 3-0T, Atlas, Participant Source Model (3-0T), Average Source Model (3-0T); Total is 1.5 only
17-5 Years 25 81 25 *Version2 will have Separate 3-0T, Atlas, Participant Source Model (3-0T), Average Source Model (3-0T); Total is 1.5 only

Adults

 
Age 1.5T 3.0T Total Notes
18-0 Years 18 20 / 107 28 Separate 3-0T, Atlas, Participant Source Model (3-0T), Average Source Model (3-0T); Total is 1.5+Version1-3.0T avg; Version1/Version2
18-5 Years 12 23 / 89 29 Separate 3-0T, Atlas, Participant Source Model (3-0T), Average Source Model (3-0T); Total is 1.5+Version1-3.0T avg; Version1/Version2
19-0 Years 10 17 / 95 23 Separate 3-0T, Atlas, Participant Source Model (3-0T), Average Source Model (3-0T); Total is 1.5+Version1-3.0T avg; Version1/Version2
19-5 Years 5 21 / 98 22 Separate 3-0T, Atlas, Participant Source Model (3-0T), Average Source Model (3-0T); Total is 1.5+Version1-3.0T avg; Version1/Version2
20-24 Years 157 108 / 316 244 Separate 3-0T, Atlas, Participant Source Model (3-0T), Average Source Model (3-0T); Total is 1.5+Version1-3.0T avg; Version1/Version2
25-29 Years 86 24 / 35 101 Separate 3-0T, Atlas, Participant Source Model (3-0T), Average Source Model (3-0T); Total is 1.5+Version1-3.0T avg; Version1/Version2
30-34 Years 63 34 / 39 79 Separate 3-0T, Atlas, Participant Source Model (3-0T), Average Source Model (3-0T); Total is 1.5+Version1-3.0T avg; Version1/Version2
35-39 Years 50 50
40-44 Years 61 61
45-49 Years 65 65
50-54 Years 57 57
55-59 Years 73 73
60-64 Years 83 83
65-69 Years 89 89
70-74 Years 101 101
75-79 Years 61 61
80-84 Years 62 62
85-89 Years 36 36

Cortical Sources


The ingredients for cortical source analysis of EEG and ERP are electrical scalp potential recordings, electrode locations, source dipole locations, and a head model. The intent of source analysis is to determine the location and strength of current dipoles located in th head that generate current on the scalp. The source dipole locations tell where the dipoles occur; and can be located in a spherical shell, on the surface of the brain, in gray matter, or in selected regions of interest.  The forward model specifies how a dipole(s) at location D with amplitude vector AM passes a current to each electrode on the scalp. The locations of the electrodes for the electrical scalp potential recordings must be known.

Four types of files are available on this site.  These files correspond to the average templates located elsewhere on the site.   1) electrode maps for 10-10 (81 electrodes) system, Geodesic Sensor Net (128 channels), and Hydrocel GSN (128 channel). These are placement locations in AC-reference origin to the average head templates;  2) source volumes for GM (sans NMA) and eyes.  These are given as MRI volumes and as EMSE 3fr wireframe files; source volumes also may be derived from the BEM models, or from atlases; 3) segmented heads for boundary element models (BEM);  three-compartment (scalp, outer skull, inner skull); four compartment (scalp, outer skull, inner skull (CSF), brain;  five compartment (scalp, outer skull, inner skull (CSF and other), GM, WM.  These are given as MRI volumes, EMSE 3fr wireframe files (four compartment), CURRY “Sn” and “Bn” files; 4) segmented heads for finite element models (FEM).   These are given as MRI volumes and EMSE 3fr wireframe files.

Some work in EMSE or CURRY will be needed or source analysis; e.g., the “forward models” in EMSE may be calculated for a FEM model with electrodes, source volume wireframe, and FEM wireframe. However, the choice of electrodes, locations of sources, and type of model need to be designed by the user.

File Structure:   Age (infant, early child, adolescent, adult) folders contain subfolders: Electrodes (AC-electrodes); BEM (boundary element model MRI volumes); FEM (segmented finite element model MRI volumes); EMSE (wireframes, elp, head and brain MRI volumes); CURRY (electrodes with fiducials, Sn and Bn model files)

Access


Terms of use: The MRI templates from this database are freely available and distributed for scientific work. The CC BY-NC-ND 3.0 license allows sharing but users should inform JER of any sharing. These should not be modified or used in commercial applications. Publications from this work should cite the publications for the data upon which these templates are based. JER retains all copyrights to the templates.

Creative Commons License
Neurodevelopmental MRI Database by John E. Richards is licensed under a Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported License.
Based on a work at http://jerlab.psych.sc.edu/NeurodevelopmentalMRIDatabase/
Instructions: The data is accessed through “SSH” protocols scp and sftp. The interested user should contact John E. Richards for a username and password.

For Linux, Unix, MAC, from a terminal:
You can get the data with “scp” or “sftp”

The easiest way is with scp:
scp -r -P 555 USERNAME@jerlab.psych.sc.edu:/ ./
Password is …
This will copy the entire data for the age group to which your password is set.

OR, use sftp:

sftp -o “Port 555” USERNAME@jerlab.psych.sc.edu
And use sftp (ftp) commands to list directories, change directories, copy specific files

From Windows, WinSCP is a free GUI that does sftp and scp (similar to GUI ftp); Hostname is jerlab.psych.sc.edu (129.252.50.187); username is your username; password; port is 555; use SFTP protocol

From MAC, CyberDuck is a free GUI that does sftp and scp (similar to GUI ftp); Hostname is jerlab.psych.sc.edu (129.252.50.187); username is your username; password; port is 555; use SFTP protocol

Note: The jerlab.psych.sc.edu should resolve to 129.252.50.187. If not, enter the IP directly.

Request Access


Requests for access to the database should be made to John E. Richards, richards-john@sc.edu .
Requests should come from full-time regular staff at academic, research, or health-care institutions (e.g., faculty, full time PhD level researchers, physicians). Requests from post-doctoral research fellows and non-doctoral level staff should be made through the regular staff mentor or supervisor.
1–please provide a brief statement describing the research that will use this resource, and the intended use of the average templates or other materials (1 to 2 sentences)
2–Please give an age range for the data. The database is separated into FirstYear, Preschool, Chilren, Adolescents, and Adults (Ages and Templates); and various combinations can be requested. The age range should be consistent with the intended usage.
3–It is ok for a person to request access for single researcher use, or for an entire laboratory. Please give some indication the number of people that may access the database.
4. Agree to terms of use: Terms of use: The MRI templates from this database are freely available and distributed for scientific work. The CC BY-NC-ND 3.0 license allows sharing but users should inform JER of any sharing. These should not be modified or used in commercial applications. Publications from this work should cite the publications for the data upon which these templates are based (Citations). JER retains all copyrights to the templates.
Creative Commons License
Neurodevelopmental MRI Database by John E. Richards is licensed under a Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported License.
Based on a work at http://jerlab.psych.sc.edu/NeurodevelopmentalMRIDatabase/
Contact John E. Richards (http:\jerlab.psych.sc.edu, richards-john@sc.edu) for access to the volumes.

Version 2


We are working on a new version of the database. The goals are to 1) increase the number of MRIs at each age the make up the averages, 2) modify some of the MRI volumes to work more seamlessly in SPM, FreeSurfer, FSL, and 3) increase the number of averages with 3T MRIs.

1) Increase the number of MRIs at each age. We are accessing several new open-access MRI sites. These include sites with young infants (e.g., IBIS), young children through adolescents (PING, CMIHBN, ABIDE, ABCD). These MRIs will be used to form new MRI averages with a minumum of about 25 participants at each age. Some of the infant ages will have more than 60 MRIs for each average.

2) Modify some of the MRI volumes. Some of the original volumes disregarded the header information or voxel orientation. This created extra steps in some programs (e.g., SPM). The header and other information will be modified to conform to accepted MRI volume standards.

3) With the addition of additional MRIs, the database will have more coverage of 3T MRI averages. We will have 3T-based averages for 3.0-Years and 4-0 through 20-24Years in 6 month increments.

Additionally, more tools will be added including scalp-to-cortex locations for use with NIRS recording, which should be very helpful for research with infant participants; eventually moving the database to an open access site such as NITRC; and possibly adding templates for children with neurodevelopmental disorders (e.g., ASD or infant ASD siblings)

These changes will be reflected in the current site with updated pages when appropriate. New averages will be added to the site when they are available. Any current versions will remain on the site and version 1 and version 2 averages will be distinguished.

Creative Commons License
Neurodevelopmental MRI Database by John E. Richards is licensed under a Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported License.
Based on a work at http://jerlab.sc.edu/NeurodevelopmentalMRIDatabase/

Contact John E. Richards (http:\\jerlab.psych.sc.edu, richards-john@sc.edu) for access to the
volumes.