Human precuneus is the most expanded medial brain area when compared with the chimpanzee
brain
Emiliano Bruner, Todd M. Preuss, Xu Chen, James K. Rilling
SUPPLEMENTARY INFORMATION
Scan procedures and templates
Female Chimpanzee Scans.
High-resolution T1-weighted images were acquired using a 3D
magnetization-prepared rapid gradient-echo (MPRAGE) sequence. The T1 scan protocol, optimized for
3T, used the following imaging parameters: a repetition time/inversion time/echo time (TR/TI/TE) of
2600/900/3.06 ms, a flip angle (FA) of 8°, a volume of view of 205×205×154 mm, a matrix of
256×256×192mm, and resolution of 0.8×0.8×0.8 mm3, with 2 averages (NEX). Total T1 scan time was
approximately 17 minutes. Five female chimpanzees (Mean Age = 25.0 yr, S.D. = 11.5 yr) were included
for individual analyses. The brain images of these chimpanzees were aligned to a chimpanzee brain
template (the template creation details below) using rigid body linear registration with 6 degree of
freedom (DoF) so that the sagittal plane was parallel to the interhemispheric fissure of the brain. Each
individual brain was then visualized in FSLVIEW and snapshots were taken of the sagittal slice that is 2.4
mm lateral from the mid-sagittal slice in both hemispheres. This specific slice was chosen to cut through
the middle of the medial parietal cortex.
Male Chimpanzee Scans. High-resolution T1-weighted images were acquired using a 3D MPRAGE
sequence. Five male chimpanzees (Mean Age = 17.2 yr, S.D. = 1.6 yr) were included in individual
analyses. The T1 scan protocols for these 5 chimpanzees are listed in table S1. As in the female
chimpanzees, brain images of these male chimpanzees were also aligned to the chimpanzee brain
template using rigid body linear registration with 6 DoF and were resampled to a consistent spatial
resolution of 0.8 mm. Each individual brain was then visualized in FSLVIEW and snapshots were
respectively taken for the sagittal slice that is 2.4 mm lateral from the mid-sagittal slice in both
hemispheres. This specific slice was chosen to cut through the middle of the medial parietal cortex.
Chimpanzee Brain Template. A population-specific template of the chimpanzee brain was created using
T1-weighted images from 36 female chimpanzees (Li et al., 2010)). Individual T1-weighted images were
preprocessed with skull stripping, intensity bias correction, noise reduction, and contrast enhancement
(squaring the images and then dividing by the mean). T1 images from a randomly selected subject were
aligned so that the sagittal plane was parallel to the interhemispheric fissure of the brain, and the axial
plane was perpendicular to the sagittal plane and parallel to the bicommissural line (the line connecting
the anterior and posterior commissures). The origin of the space was defined as the center of the anterior
commissure. All the other T1 images were aligned to the first T1 image using rigid-body registration with
6 DoF. The set of aligned T1 images was then averaged to generate an initial template. Each subject's T1
image was then registered to this initial T1 template using an affine registration with 12 DoF. These
individually aligned T1 images were subsequently averaged to create an intermediate T1 template (12
DoF) for the final alignment of the T1 images using FNIRT nonlinear registration. The brain template
was then visualized in FSLVIEW and snapshots were respectively taken for the sagittal slice that is
2.4mm lateral from the mid-sagittal slice in both hemispheres. This specific slice was chosen to cut
through the middle of the medial parietal cortex.
Human Female. T1-weighted images were acquired with a 3D MPRAGE sequence (GRAPPA factor of 2)
for all participants. The scan protocol, optimized at 3T, used a TR/TI/TE of 2600/900/3.02 ms, a flip
angle of 8°, a volume of view of 224×256×176 mm3, a matrix of 224×256×176, and a resolution of
1×1×1 mm3, with 1 average. Total T1 scan time was approximately 4 minutes. Five human females
(Mean Age = 36.8 yr, S.D. = 17.6 yr) were included for individual analysis. This age distribution of
human females matches that of the female chimpanzees, after adjusting for species differences in
longevity with a scaling factor of 1.5. Similarly, the brain images of these females were aligned to a
human brain template (template creation details below) using rigid body linear registration with 6 DoF so
that the sagittal plane was parallel to the interhemispheric fissure of the brain. Each individual brain was
then visualized in FSLVIEW and snapshots were taken of the sagittal slice that is 6.0 mm lateral from the
mid-sagittal slice in both hemispheres. This specific slice was chosen to cut through the middle of the
medial parietal cortex.
Human Male. T1-weighted images were acquired with a 3D MPRAGE sequence (GRAPPA factor of 2)
for all participants. The scan protocol, optimized at 3T, used a TR/TI/TE of 2600/900/3.02 ms, a flip
angle of 8°, a volume of view of 256×256×176 mm3, a matrix of 256×256×176, and a resolution of
1×1×1 mm3, with 1 average. Total T1 scan time was approximately 4 minutes. Five age-matched human
males (Mean Age = 26.2 yr, S.D. = 2.2yr) were included for individual analysis. As in the human
females, brain images of these males were aligned to the human brain template using rigid body linear
registration with 6 DoF so that the sagittal plane was parallel to the interhemispheric fissue of the brain.
Each individual brain was then visualized in FSLVIEW and snapshots were respectively taken for the
sagittal slice that is 6.0 mm lateral from the mid-sagittal slice in both hemispheres. This specific slice was
chosen to cut through the middle of the medial parietal cortex.
Human Brain Template. A population-specific brain template of the human was created based on the T1weighted images from 40 human females using groupwise registration (Fonov et al., 2011). Individual
T1-weighted images were preprocessed with skull stripping, intensity bias correction, noise reduction,
and contrast enhancement (squaring the images and then dividing by the mean). All T1 images were first
aligned to the MNI T1 template using rigid-body registration with 6 DoF. The set of aligned T1 images
was then averaged to generate an initial template. This initial T1 template was then nonlinearly registered
to each subject's T1 image using FNIRT. The inverse warp for all subjects were then averaged to obtain a
mean deformation warp, which then applied to each subject's T1 image together with the individual
inverse warp. These warped T1 images were subsequently averaged to create an intermediate T1
template. The above nonlinear registration procedure will be repeated and the final unbiased human T1
template will be obtained after four iterations at five decreasing levels of subsampling and blurring
kernels. The brain template was then visualized in FSLVIEW and snapshots were respectively taken for
the sagittal slice that is 6.0 mm lateral from the mid-sagittal slice in both hemispheres. This specific slice
was chosen to cut through the middle of the medial parietal cortex.
References
Li L, Preuss TM, Rilling JK, Hopkins WD, Glasser MF, Kumar B, Nana R, Zhang X, Hu X (2010)
Chimpanzee (Pan troglodytes) precentral corticospinal system asymmetry and handedness: a diffusion
magnetic resonance imaging study. PLoS ONE 5:e12886.
Fonov V, Evans AC, Botteron K, Almli CR, McKinstry RC, Collins DL, Brain Development Cooperative
Group (2011) Unbiased average age-appropriate atlases for pediatric studies. Neuroimage 54:313-27.
Table: MPRAGE T1 protocol for 5 male chimpanzees
Animals
TR/TE/TI(ms)
Spatial
FA
NEX
MATRIX
FOV(mm)
Chimpanzee 1 2300/4.38/1100
8
2
512×512×192
307×307×115
0.6
Chimpanzee 2 2300/4.38/1100
8
2
256×256×192
256×256×192
1
Chimpanzee 3 2300/4.38/1100
8
2
256×256×192
256×256×192
1
Chimpanzee 4
2600/3.93/900
8
1
256×224×176
256×224×176
1
Chimpanzee 5
?
8
2
286×286×165
200×200×115
0.7
Resolution(mm)