Methods for High Resolution Ex Vivo Brain Anatomical MR Imaging
Presented During: Poster Session 3
Friday, June 27, 2025: 01:45 PM - 03:45 PM
Friday, June 27, 2025: 01:45 PM - 03:45 PM
Presented During: Poster Session 4
Saturday, June 28, 2025: 01:45 PM - 03:45 PM
Saturday, June 28, 2025: 01:45 PM - 03:45 PM
Poster No:
1876
Submission Type:
Late-Breaking Abstract Submission
Authors:
Andre van der Kouwe1, Robert Frost1, Divya Varadarajan1, Yael Balbastre2, Jean Augustinack1, Kathryn Evancic1, Jackson Nolan1, Allison Stevens Player1, Cole Analoro1, Lucas Deden Binder1, Jocelyn Mora1, Jingting Yao1, Azma Mareyam1, M Tisdall3, Paul Wighton1, Brian Edlow1, C. Dirk Keene4, Susie Huang1, Bruce Fischl1
Institutions:
1Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Boston, MA, 2Department of Experimental Psychology, University College London, London, Greater London, 3University of Pennsylvania, Philadelphia, PA, 4University of Washington, Seattle, WA
First Author:
Andre van der Kouwe
Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital
Boston, MA
Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital
Boston, MA
Co-Author(s):
Robert Frost
Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital
Boston, MA
Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital
Boston, MA
Divya Varadarajan
Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital
Boston, MA
Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital
Boston, MA
Yael Balbastre
Department of Experimental Psychology, University College London
London, Greater London
Department of Experimental Psychology, University College London
London, Greater London
Jean Augustinack
Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital
Boston, MA
Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital
Boston, MA
Kathryn Evancic
Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital
Boston, MA
Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital
Boston, MA
Jackson Nolan
Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital
Boston, MA
Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital
Boston, MA
Allison Stevens Player
Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital
Boston, MA
Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital
Boston, MA
Cole Analoro
Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital
Boston, MA
Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital
Boston, MA
Lucas Deden Binder
Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital
Boston, MA
Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital
Boston, MA
Jocelyn Mora
Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital
Boston, MA
Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital
Boston, MA
Jingting Yao
Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital
Boston, MA
Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital
Boston, MA
Azma Mareyam
Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital
Boston, MA
Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital
Boston, MA
Paul Wighton
Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital
Boston, MA
Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital
Boston, MA
Brian Edlow
Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital
Boston, MA
Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital
Boston, MA
Susie Huang
Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital
Boston, MA
Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital
Boston, MA
Bruce Fischl
Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital
Boston, MA
Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital
Boston, MA
Late Breaking Reviewer(s):
Introduction:
Interest in imaging brain tissue samples ("ex vivo imaging") with MRI has increased substantially over the last several years. MRI is non-invasive and non-destructive, and the images are continuous in three dimensions. While neither the resolution nor the contrast competes with histology, MRI offers multiple useful contrasts at the mesoscale between in vivo imaging and histology, thus bridging the divide between pathology observed at the microscopic scale and what is observable with MRI in clinical practice. Ex vivo MRI also provides vascular and connectivity information across the whole brain. In this abstract we present acquisition and processing methods for whole brain MRI parameter mapping at resolutions of 120 µm isotropic.
Methods:
Brain samples are packed in MR-invisible liquid perfluorocarbon in a plastic bag, while minimizing air bubbles. Perfluorocarbon is the preferred medium as the brain outer surface is well defined relative to the dark background in the resulting images, and artifacts due to bubbles in the fluid are reduced.
Samples are scanned in a 7 T Siemens Terra.X MRI scanner with a custom 31-channel ex vivo coil (Edlow, 2019). To characterize the anatomy, we obtain T1-weighted FLASH volumes with multiple flip angles and echo times, from which we quantify PD, and T1 and T2* relaxation times. Before parameter fitting, we correct the images for B0-related distortions and B1+ inhomogeneities.
The 120 µm FLASH protocol is as follows: TE 10/20/30/40 ms, TR 55 ms, FA 10/20/40˚, BW 110 Hz/px, matrix 1536 x 1344, 1280 slices. Scanner RAM is insufficient for online image reconstruction and the scanner internal RAID is insufficient to store the k-space data for a single scan (~ 3 TB). Therefore, we divide the scan into 8 segments (phase encoding subsets) and stream the data offline during the scan (see Figure 1). Since the resonance frequency changes with time, we collect 4 overlapping k-space slices at the edges of segments to correct the phase variation across k-space. This eliminates blurring that most commonly occurs in the first high resolution scan.
A conventional 2D B0 map is acquired: TE 2.2/3.22 ms, TR 5 s, 1.23 mm3 resolution. However, the resolution of this map is insufficient to correct local susceptibility-related distortions accurately in the high-resolution scan. Therefore, we correct distortions using TOPUP (Andersson, 2003). This requires that at least one flip angle of the high-resolution scan be collected twice, with opposite readout gradient polarity. If this scan is not available, we synthesize the "missing" scan from the even and odd echoes. For example, averaging the first and third echoes approximates the second echo, but with opposite readout polarity/distortion. Additionally, we apply TOPUP with an error metric that emphasizes edges using an algorithm called EPIC (Varadarajan, 2020).
The B1+ transmit profile is inhomogeneous at 7 T. Fast B1+ mapping methods such as AFI proved inaccurate and so we use a conventional but slow technique of 2D FLASH (2 mm resolution) with varying transmit voltage. We fit the sinusoid at each voxel to determine the local flip angle. To estimate PD and T1, we solve the FLASH steady-state equation (Fischl, 2004; Deoni, 2007) across scans with different flip angles, correcting the flip angles at each voxel using the B1+ map.
Samples are scanned in a 7 T Siemens Terra.X MRI scanner with a custom 31-channel ex vivo coil (Edlow, 2019). To characterize the anatomy, we obtain T1-weighted FLASH volumes with multiple flip angles and echo times, from which we quantify PD, and T1 and T2* relaxation times. Before parameter fitting, we correct the images for B0-related distortions and B1+ inhomogeneities.
The 120 µm FLASH protocol is as follows: TE 10/20/30/40 ms, TR 55 ms, FA 10/20/40˚, BW 110 Hz/px, matrix 1536 x 1344, 1280 slices. Scanner RAM is insufficient for online image reconstruction and the scanner internal RAID is insufficient to store the k-space data for a single scan (~ 3 TB). Therefore, we divide the scan into 8 segments (phase encoding subsets) and stream the data offline during the scan (see Figure 1). Since the resonance frequency changes with time, we collect 4 overlapping k-space slices at the edges of segments to correct the phase variation across k-space. This eliminates blurring that most commonly occurs in the first high resolution scan.
A conventional 2D B0 map is acquired: TE 2.2/3.22 ms, TR 5 s, 1.23 mm3 resolution. However, the resolution of this map is insufficient to correct local susceptibility-related distortions accurately in the high-resolution scan. Therefore, we correct distortions using TOPUP (Andersson, 2003). This requires that at least one flip angle of the high-resolution scan be collected twice, with opposite readout gradient polarity. If this scan is not available, we synthesize the "missing" scan from the even and odd echoes. For example, averaging the first and third echoes approximates the second echo, but with opposite readout polarity/distortion. Additionally, we apply TOPUP with an error metric that emphasizes edges using an algorithm called EPIC (Varadarajan, 2020).
The B1+ transmit profile is inhomogeneous at 7 T. Fast B1+ mapping methods such as AFI proved inaccurate and so we use a conventional but slow technique of 2D FLASH (2 mm resolution) with varying transmit voltage. We fit the sinusoid at each voxel to determine the local flip angle. To estimate PD and T1, we solve the FLASH steady-state equation (Fischl, 2004; Deoni, 2007) across scans with different flip angles, correcting the flip angles at each voxel using the B1+ map.
·Figure 1: Configuration of scanner with data streaming
Results:
We scanned four whole brains at 120 um and applied the above pipeline (Figure 2). The data will be made public on the FITBIR archive. In some cases, we observe bulk sample motion of a fraction of a millimeter/degree of rotation, and we observe bubble movement during scans. We are exploring methods, including embedded navigators, to track sample motion.
·Figure 2: (Left) Inputs to processing pipeline: 3 flip angles x 4 echoes, displacement (~B0) map, and B1+ map. (Right) Outputs: proton density map, and T1 and T2* relaxation parameter maps (zoomed)
Conclusions:
Our pipeline facilitates accurate MR imaging of brain samples. We are working on further processing, including vessel segmentation and registration with histology. The sequences and processing pipeline are available.
This work was supported in part by NIH U24NS135561.
This work was supported in part by NIH U24NS135561.
Neuroanatomy, Physiology, Metabolism and Neurotransmission:
Neuroanatomy Other 2
Novel Imaging Acquisition Methods:
Anatomical MRI 1
Keywords:
Acquisition
Cortical Layers
Morphometrics
STRUCTURAL MRI
Other - Ex vivo MRI
1|2Indicates the priority used for review
Abstract Information
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Provide references using APA citation style.
Andersson, JLR (2003). How to correct susceptibility distortions in spin-echo echo-planar images: application to diffusion tensor imaging. NeuroImage, 20(2):870-888.
Varadarajan, D (2020). Edge-preserving B0 inhomogeneity distortion correction for high-resolution multi-echo ex vivo MRI at 7T. 28th Meeting of the ISMRM, Paris, France.
Fischl, B (2004). Sequence-independent segmentation of magnetic resonance images. Neuroimage. 23.
Deoni, SC (2007). High-resolution T1 mapping of the brain at 3T with driven equilibrium single pulse observation of T1 with high-speed incorporation of RF field inhomogeneities (DESPOT1-HIFI). J Magn Reson Imaging. 26(4).