High-resolution awake mouse fMRI at 14 tesla

  1. David Hike
  2. Xiaochen Liu
  3. Zeping Xie
  4. Bei Zhang
  5. Sangcheon Choi
  6. Xiaoqing Alice Zhou
  7. Andy Liu
  8. Alyssa Murstein
  9. Yuanyuan Jiang
  10. Anna Devor
  11. Xin Yu  Is a corresponding author
  1. Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Harvard Medical School, Massachusetts General Hospital, United States
  2. Graduate Program in Neuroscience, Boston University, United States
  3. Department of Biomedical Engineering, Boston University, United States
8 figures, 2 videos, 3 tables and 1 additional file

Figures

Figure 1 with 2 supplements
Comparison between implanted and commercial coils.

(A and B) show representative (unattached) prototype coils in the single loop and ‘figure 8’ styles, respectively. (C) Box-and-whisker plot presents the cortical-specific signal-to-noise ratio (SNR) …

Figure 1—figure supplement 1
Schematic of circuit diagram of coil designed for 1H imaging at 600 MHz.

C1 and C4 are 2.2 pF capacitors. C2 is a 0.6–2.5 pF trimmer. C3 is a 5–18 pF trimmer.

Figure 1—figure supplement 2
Comparison between implanted and commercial coils.

(A) shows representative (unimplanted) coils in the single loop (left) and ‘figure 8’ styles (right). Table 2 provides a parts list and cost for making these coils and Figure 1—figure supplement 1

Figure 2 with 2 supplements
High-resolution awake mouse functional magnetic resonance imaging (fMRI) at 14 T.

(A). The awake mouse setup with head-fixed position in a custom-built cradle for visual and vibrissa stimulation. (B) The representative fMRI time course of an awake mouse based on raw image data …

Figure 2—figure supplement 1
Results of acclimation training on animals.

(A) Box-and-whisker plot showing eye movements over 10 min duration of training days showing an increase in eye movements over the training duration indicating the animals are becoming more relaxed …

Figure 2—figure supplement 2
Figure showing motion data (.MOT file) of a representative mouse immediately following training (A) and after 1 month of scanning (B) indicating the amount of struggling the animal is doing during scanning.

Struggling-induced spikes are already substantially minimized following the training with only 5 volumes (2%) censored. After 1 month of scanning there was only one single repetition (repetition …

Figure 3 with 3 supplements
Visual stimulation-evoked high-resolution functional magnetic resonance imaging (fMRI) of awake mice.

(A) The brain-wide functional maps of awake mice show strong positive blood oxygen level-dependent (BOLD) activation in the visual cortex (VC), lateral geniculate nucleus (LGN), superior colliculus …

Figure 3—figure supplement 1
Figure showing stimulation paradigm in blue.

Each ‘TR period’ is 2 s. The stimulation is repeated 10 times over the 410 s acquisition period which includes a 10 s baseline acquisition period before the first stimulation. This paradigm results …

Figure 3—figure supplement 2
The processing pipeline of the awake mouse functional magnetic resonance imaging (fMRI) datasets.

The workflow diagram is described through the following steps: raw data registration, outlier removal, volume registration-based motion file estimation, motion removal, linear regression with the …

Figure 3—figure supplement 3
Time course from single experiment showing strong blood oxygen level-dependent (BOLD) activations during stimulation paradigm.

(Left) BOLD activation map highlighting positive activation in the barrel cortex (BC) and selection of a 3×3 voxel display of time course data (green box). (Right) Time course data taken from 3×3 …

Vibrissa stimulation-evoked high-resolution functional magnetic resonance imaging (fMRI) of awake mice.

(A) The brain-wide functional maps of awake mice show the strong positive blood oxygen level-dependent (BOLD) activation in the contralateral barrel cortex (BC) and ventral posteromedial nucleus …

Ventral retrosplenial area (VRA)-based brain-wide correlation maps at different time shifts.

(A) The VRA-based correlation maps at –6 s and 0 s time shifts of awake mice with repetitive stimulation (REP). The strong correlation in the contralateral barrel cortex (BC) is shown in the …

Author response image 1
Comparison between implanted and commercial coils.

(A) shows representative coils in the single loop (left) and ‘figure 8’ styles (right). Supplementary Table 1 provides a parts list and cost for making these coils and Supplementary Figure 1 …

Author response image 2
The eye movements (A) and power spectra of pupil dynamics (<0.02Hz) (B) change during different training phases.
Author response image 3
Representative images are shown indicating connections between the barrel cortex and retrosplenial area from an injection in the barrel cortex (Left panel) as well as the visual cortex and cingulate connection from an injection in the visual cortex (Right panel).

Images are of connectivity map projections from the Allen Brain Atlas derived from a Cre-dependent AAV tracing of axonal projections (Oh et al., 2014)

Videos

Video 1
Video illustrating how animals are set up through the cradle using the implanted radio frequency (RF) coil for awake mouse imaging.
Video 2
Video showing the real-time EPI raw images from awake mice.

The real-time tracer from the selected point demonstrates the time points with motion, as well as the motion-induced image distortion during awake mouse fMRI.

Tables

Table 1
Table showing the training paradigm for each of the four phases of training.

rs → resting-state fMRI, stim → whisker stimulation fMRI.

Training day of phasePhase 1(hold in hand)Phase 2(holder+pupil)Phase 3(mock-MRI+pupil)Phase 4(EPI+pupil)
15 min15 min30 min60 min (rs)
210 min30 min30 min60 min (rs)
330 min60 min (stim)
430 min60 min (stim)
560 min
660 min
760 min
860 min
Table 2
Parts list for construction of 200 1H coils configured for 600 MHz (14 T).
Part descriptionCost
FR-4 PCB Chip, 0.4×0.8 in, 0.062 in thick$214.00/200
Capacitor 2.2 pF 2KV$309.80/400
Trimmer 0.6–2.5 pF$1649.28/200
Trimmer 5–18 pF$1640.56/200
Magnet wire 20AWG$118.28/spool/710.8’
MCX socket$1027.14/200
Entire coil built by MRIBOT$300/each
Author response table 1
Training Day of Each PhasePhase 1 (hold in hand)Phase 2 (holder +pupil)Phase 3 (Mock-MRI+pupil)Phase 4 (EPI +pupil)
15 mins15 mins30 mins60 mins (rs)
210 mins30 mins30 mins60 mins (rs)
330 mins60 mins (stim)
430 mins60 mins (stim)
560 mins
660 mins
760 mins
860 mins

Additional files

Download links