Mapping the human subcortical auditory system using histology, postmortem MRI and in vivo MRI at 7T
- Massachusetts Institute of Technology, United States
- Harvard University, United States
- Maastricht University, Netherlands
- Duke University, United States
- University of Minnesota, United States
Figures
Figure 1
Literature diagrams (left columns) redrawn from Moore (1987) for the cochlear nucleus (CN), superior olivary complex (SOC), inferior colliculus (IC) and from the Allen Human Brain Atlas (Hawrylycz et al., 2012) for the medial geniculate body (MGB) compared to similar cuts from histology (BigBrain) in MNI (central column) and 3-D reconstructions of the segmented structures from the histology (bottom right column).
The auditory structures are highlighted in gray in the left column, by a dotted line in the central column and in red on the modified Gray’s anatomy Plate 719 (Gray and Lewis, 1918) and rendered as …
Figure 2
BigBrain—7T postmortem MRI image comparisons.
Histological data (BigBrain) (left column) and T2*-weighted postmortem MRI data (100 µm - central column) in MNI space. Panels from bottom to top are chosen to highlight subcortical auditory …
Figure 3 with 3 supplements
Postmortem diffusion MRI tractography.
Left: streamlines passing through subcortical auditory structures, defined from 50 µm post mortem MRI in the same specimen, warped to 200µm isotropic diffusion image space and dilated 2.5 voxels …
Figure 3—figure supplement 1
Postmortem tractography with undilated ROIs.
Postmortem human diffusion-weighted MRI tractography (from 200 µm isotropic voxels) with anatomically defined subcortical auditory seeds, downsampled to 200 µm but undilated. Streamlines that passed …
Figure 3—figure supplement 2
Postmortem tractography using data downsampled to in vivo resolution (1.05 mm).
Postmortem human diffusion-weighted MRI tractography with anatomically defined subcortical auditory seeds. MRI data were downsampled from 200 µm to 1050 µm to match in vivo data acquisition and then …
Figure 3—video 1
360° rotation video of postmortem streamlines.
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Figure 4 with 5 supplements
Single subject functional activation maps obtained from Experiment one thresholded for significance (FDR-q = 0.05 and p<0.001; see Materials and methods for details) and leave-one-out probabilistic functional maps highlighting voxels that are significant in at least three of the other nine subjects.
For each participant, CN/SOC and IC are shown in transversal cuts, MGB is shown in a coronal cut. See single subject videos for 3-D view of these maps in Figure 10 supplements. Unthresholded maps …
Figure 4—figure supplement 1
Correspondence between single subject activation maps and leave-one-out probabilistic maps.
Correspondence between single subject activation maps and leave-one-out functional probabilistic maps. Leave-one-out probabilistic functional maps are thresholded to identify voxels that are …
Figure 4—figure supplement 2
Effect of threshold on leave-one-out probabilistic maps on correspondence with single subject activations].
Correspondence between single subject activation maps and leave-one-out functional probabilistic maps at different thresholds. Leave-one-out probabilistic functional maps are thresholded to identify …
Figure 4—figure supplement 3
Reproducibility across experiments of the functional activation maps in six participants (also see Figure 11).
Reproducibility of functional activation maps. Functional activation maps obtained from Experiment one and Experiment 2 (six participants) thresholded for significance (FDR-q = 0.05 and p<0.001; see …
Figure 4—figure supplement 4
Correspondence between single subject activation maps across experiments.
Correspondence between single subject activation maps Experiment one and Experiment 2. All maps are thresholded for significance (FDR-q = 0.05 and p<0.001; see Materials and methods for details). …
Figure 4—figure supplement 5
Effect of spatial smoothing in the analysis of the data collected from two of the participants.
Effect of spatial smoothing on functional activation maps. Functional activation maps obtained from Experiment one in two participants with and without applying spatial smoothing (1.5 mm FWHM …
Figure 5 with 2 supplements
In vivo functional MRI responses to auditory stimuli, combined across 10 participants.
Left column: Conjunction of participants plotted on top of one participant’s short inversion T1-weighted anatomical MRI. Center column: Conjunction of participants’ fMRI responses warped to MNI …
Figure 5—figure supplement 1
In vivo anatomical group average images in MNI space.
In vivo anatomical group average images in MNI space.
Figure 5—figure supplement 2
Anatomical images from MNI ICBM 152 compared to BigBrain in MNI space Anatomical images from MNI ICBM 152 2009b dataset compared to BigBrain histology in MNIspace (left column).
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Figure 6 with 2 supplements
In vivo tractography of the subcortical auditory system from 7T diffusion-weighted MRI.
Left: 3-D images from one participant. Fiber orientation distribution functions were estimated from diffusion-weighted MRI images of the brainstem and were used for deterministic tractography. …
Figure 6—figure supplement 1
Bar plot of streamline counts through each ROI.
Diffusion-weighted MRI tractography streamlines passing through each subcortical auditory region of interest for the ten in vivo participants. Bars represent 95% confidence intervals.
Figure 6—video 1
360° rotation video of in vivo streamlines.
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Figure 7
The registration error around the inferior colliculus is visible bilaterally when comparing Panel 2 and Panel 3.
The dashed lines indicate the correct shape (and location) of the colliculi in MNI space. The arrows point to the inferior colliculus (IC). The last panel shows the corrected BigBrain MNI dataset.
Figure 8
Summary of data processing steps, including availability of data and code.
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Figure 9 with 1 supplement
One frame of volume rendered animations for comparing histology (BigBrain), post-mortem MRI, in-vivo MRI unthresholded positive t-values group average and in-vivo MRI clusters of significant activity overlapping in at least four subjects in each voxel.
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Figure 9—video 1
3D volume rendered comparisons in MNI space.
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Figure 10 with 10 supplements
One frame of volume rendered animations for single subject statistical maps.
(Left)positive t-values (middle) after thresholding (right) leave-one-out probabilistic map ()). Viewing angle here is similar to Figure 1.
Figure 10—video 1
Subject 01.
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Figure 10—video 2
Subject 02.
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Figure 10—video 3
Subject 03.
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Figure 10—video 4
Subject 05.
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Figure 10—video 5
Subject 06.
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Figure 10—video 6
Subject 07.
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Figure 10—video 7
Subject 08.
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Figure 10—video 8
Subject 09.
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Figure 10—video 9
Subject 10.
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Figure 10—video 10
Subject 11.
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Figure 11 with 7 supplements
One frame of volume rendered animations for Subject 01 statistical maps (experiment 1 positive t-values and thresholded (col 1–2) and experiment 2 positive t-values and thresholded (col 3–4)).
Viewing angle here is similar to Figure 1.
Figure 11—video 1
Subject 01 experiment 1 vs experiment 2.
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Figure 11—video 2
Subject 02 experiment 1 vs experiment 2.
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Figure 11—video 3
Subject 05 experiment 1 vs experiment 2.
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Figure 11—video 4
Subject 09 experiment 1 vs experiment 2.
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Figure 11—video 5
Subject 10 experiment 1 vs experiment 2.
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Figure 11—video 6
Subject 11 experiment 1 vs experiment 2.
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Figure 11—video 7
Group average (N=6) unthresholded positive t-values for experiment 1 vs experiment 2.
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Author response image 1
Underlay image: BigBrain histology in MNI152 space.
Yellow overlay: mask of post mortem anatomical MRI in MNI152 space.
Author response image 2
Underlay image: BigBrain histology in MNI152 space.
Segmentation overlay: conjunction of two raters’ IC segmentations based on post mortem anatomical MRI (conducted in native space) in MNI152 space.
Videos
Author response video 1
Group average fMRI results from two separate experiments.
https://doi.org/10.7554/eLife.48932.047
Author response video 2
In vivo probabilistic tractography of the subcortical auditory system in one individual.
https://doi.org/10.7554/eLife.48932.050Tables
Table 1
Comparisons between the volume (mm3) of auditory subcortical structures reported in the literature (Glendenning and Masterton, 1998) and the volume obtained in our BigBrain segmentation (in MNI space), post mortem MRI data segmentation and in vivo functional clusters (defined based on voxels that are significant in at least three, four, or five participants out of the 10 included in Experiment 1).
https://doi.org/10.7554/eLife.48932.004| Literature | BigBrain | Post mortem | In vivo (thr=3) | In vivo (thr=4) | In vivo (thr=5) | |
|---|---|---|---|---|---|---|
| CN | 46 | 32 | 11 | 54 | 24 | 11 |
| SOC | 7 | 6 | 4 | 124 | 63 | 29 |
| IC | 65 | 63 | 73 | 263 | 189 | 146 |
| MGN | 58 | 75 | 134 | 304 | 207 | 152 |
Additional files
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Transparent reporting form
- https://doi.org/10.7554/eLife.48932.044
