1
|
Sun K, Chen Z, Dan G, Luo Q, Yan L, Liu F, Zhou XJ. Three-dimensional echo-shifted EPI with simultaneous blip-up and blip-down acquisitions for correcting geometric distortion. Magn Reson Med 2023; 90:2375-2387. [PMID: 37667533 PMCID: PMC10903279 DOI: 10.1002/mrm.29828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 07/08/2023] [Accepted: 07/25/2023] [Indexed: 09/06/2023]
Abstract
PURPOSE EPI with blip-up/down acquisition (BUDA) can provide high-quality images with minimal distortions by using two readout trains with opposing phase-encoding gradients. Because of the need for two separate acquisitions, BUDA doubles the scan time and degrades the temporal resolution when compared to single-shot EPI, presenting a major challenge for many applications, particularly fMRI. This study aims at overcoming this challenge by developing an echo-shifted EPI BUDA (esEPI-BUDA) technique to acquire both blip-up and blip-down datasets in a single shot. METHODS A 3D esEPI-BUDA pulse sequence was designed by using an echo-shifting strategy to produce two EPI readout trains. These readout trains produced a pair of k-space datasets whose k-space trajectories were interleaved with opposite phase-encoding gradient directions. The two k-space datasets were separately reconstructed using a 3D SENSE algorithm, from which time-resolved B0 -field maps were derived using TOPUP in FSL and then input into a forward model of joint parallel imaging reconstruction to correct for geometric distortion. In addition, Hankel structured low-rank constraint was incorporated into the reconstruction framework to improve image quality by mitigating the phase errors between the two interleaved k-space datasets. RESULTS The 3D esEPI-BUDA technique was demonstrated in a phantom and an fMRI study on healthy human subjects. Geometric distortions were effectively corrected in both phantom and human brain images. In the fMRI study, the visual activation volumes and their BOLD responses were comparable to those from conventional 3D echo-planar images. CONCLUSION The improved imaging efficiency and dynamic distortion correction capability afforded by 3D esEPI-BUDA are expected to benefit many EPI applications.
Collapse
Affiliation(s)
- Kaibao Sun
- Center for Magnetic Resonance Research, University of Illinois at Chicago, Chicago, IL, United States
| | - Zhifeng Chen
- USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- Department of Data Science and AI, Faculty of IT, Monash University, Clayton, VIC, Australia
| | - Guangyu Dan
- Center for Magnetic Resonance Research, University of Illinois at Chicago, Chicago, IL, United States
- Department of Biomedical Engineering, University of Illinois at Chicago, Chicago, IL, United States
| | - Qingfei Luo
- Center for Magnetic Resonance Research, University of Illinois at Chicago, Chicago, IL, United States
| | - Lirong Yan
- USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- Department of Radiology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Feng Liu
- School of Information Technology and Electrical Engineering, The University of Queensland, Brisbane, Queensland, Australia
| | - Xiaohong Joe Zhou
- Center for Magnetic Resonance Research, University of Illinois at Chicago, Chicago, IL, United States
- Department of Biomedical Engineering, University of Illinois at Chicago, Chicago, IL, United States
- Departments of Radiology and Neurosurgery, University of Illinois at Chicago, Chicago, IL, United States
| |
Collapse
|
2
|
Naser MA, Wahid KA, Ahmed S, Salama V, Dede C, Edwards BW, Lin R, McDonald B, Salzillo TC, He R, Ding Y, Abdelaal MA, Thill D, O'Connell N, Willcut V, Christodouleas JP, Lai SY, Fuller CD, Mohamed ASR. Quality assurance assessment of intra-acquisition diffusion-weighted and T2-weighted magnetic resonance imaging registration and contour propagation for head and neck cancer radiotherapy. Med Phys 2023; 50:2089-2099. [PMID: 36519973 PMCID: PMC10121748 DOI: 10.1002/mp.16128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 11/10/2022] [Accepted: 11/13/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND/PURPOSE Adequate image registration of anatomical and functional magnetic resonance imaging (MRI) scans is necessary for MR-guided head and neck cancer (HNC) adaptive radiotherapy planning. Despite the quantitative capabilities of diffusion-weighted imaging (DWI) MRI for treatment plan adaptation, geometric distortion remains a considerable limitation. Therefore, we systematically investigated various deformable image registration (DIR) methods to co-register DWI and T2-weighted (T2W) images. MATERIALS/METHODS We compared three commercial (ADMIRE, Velocity, Raystation) and three open-source (Elastix with default settings [Elastix Default], Elastix with parameter set 23 [Elastix 23], Demons) post-acquisition DIR methods applied to T2W and DWI MRI images acquired during the same imaging session in twenty immobilized HNC patients. In addition, we used the non-registered images (None) as a control comparator. Ground-truth segmentations of radiotherapy structures (tumour and organs at risk) were generated by a physician expert on both image sequences. For each registration approach, structures were propagated from T2W to DWI images. These propagated structures were then compared with ground-truth DWI structures using the Dice similarity coefficient and mean surface distance. RESULTS 19 left submandibular glands, 18 right submandibular glands, 20 left parotid glands, 20 right parotid glands, 20 spinal cords, and 12 tumours were delineated. Most DIR methods took <30 s to execute per case, with the exception of Elastix 23 which took ∼458 s to execute per case. ADMIRE and Elastix 23 demonstrated improved performance over None for all metrics and structures (Bonferroni-corrected p < 0.05), while the other methods did not. Moreover, ADMIRE and Elastix 23 significantly improved performance in individual and pooled analysis compared to all other methods. CONCLUSIONS The ADMIRE DIR method offers improved geometric performance with reasonable execution time so should be favoured for registering T2W and DWI images acquired during the same scan session in HNC patients. These results are important to ensure the appropriate selection of registration strategies for MR-guided radiotherapy.
Collapse
Affiliation(s)
- Mohamed A Naser
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Kareem A Wahid
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Sara Ahmed
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Vivian Salama
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Cem Dede
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Benjamin W Edwards
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ruitao Lin
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Brigid McDonald
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Travis C Salzillo
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Renjie He
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Yao Ding
- Department of Radiation Physics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Moamen Abobakr Abdelaal
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | | | | | | | - Stephen Y Lai
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Clifton D Fuller
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Abdallah S R Mohamed
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| |
Collapse
|
3
|
Unno K, Sumiyoshi A, Konishi T, Hayashi M, Taguchi K, Muguruma Y, Inoue K, Iguchi K, Nonaka H, Kawashima R, Hasegawa-Ishii S, Shimada A, Nakamura Y. Theanine, the Main Amino Acid in Tea, Prevents Stress-Induced Brain Atrophy by Modifying Early Stress Responses. Nutrients 2020; 12:nu12010174. [PMID: 31936294 PMCID: PMC7019546 DOI: 10.3390/nu12010174] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 12/30/2019] [Accepted: 01/04/2020] [Indexed: 11/16/2022] Open
Abstract
Chronic stress can impair the health of human brains. An important strategy that may prevent the accumulation of stress may be the consumption of functional foods. When senescence-accelerated mice prone 10 (SAMP10), a stress-sensitive strain, were loaded with stress using imposed male mouse territoriality, brain volume decreased. However, in mice that ingested theanine (6 mg/kg), the main amino acid in tea leaves, brain atrophy was suppressed, even under stress. On the other hand, brain atrophy was not clearly observed in a mouse strain that aged normally (Slc:ddY). The expression level of the transcription factor Npas4 (neuronal PAS domain protein 4), which regulates the formation and maintenance of inhibitory synapses in response to excitatory synaptic activity, decreased in the hippocampus and prefrontal cortex of stressed SAMP10 mice, but increased in mice that ingested theanine. Lipocalin 2 (Lcn2), the expression of which increased in response to stress, was significantly high in the hippocampus and prefrontal cortex of stressed SAMP10 mice, but not in mice that ingested theanine. These data suggest that Npas4 and Lcn2 are involved in the brain atrophy and stress vulnerability of SAMP10 mice, which are prevented by the consumption of theanine, causing changes in the expression of these genes.
Collapse
Affiliation(s)
- Keiko Unno
- Tea Science Center, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan; (M.H.); (K.T.); (Y.N.)
- School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan;
- Correspondence: ; Tel.: +81-54-264-5822
| | - Akira Sumiyoshi
- Institute of Development, Aging and Cancer, Tohoku University, 4-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan; (A.S.); (H.N.); (R.K.)
- National Institutes for Quantum and Radiological Science and Technology, 4-9-1, Anagawa, Inage-ku, Chiba 263-8555, Japan
| | - Tomokazu Konishi
- Faculty of Bioresource Sciences, Akita Prefectural University, Shimoshinjo Nakano, Akita 010-0195, Japan;
| | - Michiko Hayashi
- Tea Science Center, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan; (M.H.); (K.T.); (Y.N.)
| | - Kyoko Taguchi
- Tea Science Center, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan; (M.H.); (K.T.); (Y.N.)
| | - Yoshio Muguruma
- College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan; (Y.M.); (K.I.)
| | - Koichi Inoue
- College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan; (Y.M.); (K.I.)
| | - Kazuaki Iguchi
- School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan;
| | - Hiroi Nonaka
- Institute of Development, Aging and Cancer, Tohoku University, 4-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan; (A.S.); (H.N.); (R.K.)
| | - Ryuta Kawashima
- Institute of Development, Aging and Cancer, Tohoku University, 4-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan; (A.S.); (H.N.); (R.K.)
| | - Sanae Hasegawa-Ishii
- Faculty of Health Sciences, Kyorin University, 5-4-1 Shimorenjaku, Mitaka, Tokyo 181-8612, Japan; (S.H.-I.); (A.S.)
| | - Atsuyoshi Shimada
- Faculty of Health Sciences, Kyorin University, 5-4-1 Shimorenjaku, Mitaka, Tokyo 181-8612, Japan; (S.H.-I.); (A.S.)
| | - Yoriyuki Nakamura
- Tea Science Center, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan; (M.H.); (K.T.); (Y.N.)
| |
Collapse
|
4
|
Usman M, Kakkar L, Matakos A, Kirkham A, Arridge S, Atkinson D. Joint B 0 and image estimation integrated with model based reconstruction for field map update and distortion correction in prostate diffusion MRI. Magn Reson Imaging 2020; 65:90-99. [PMID: 31655138 PMCID: PMC6837878 DOI: 10.1016/j.mri.2019.09.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 07/15/2019] [Accepted: 09/15/2019] [Indexed: 12/24/2022]
Abstract
In prostate Diffusion Weighted MRI, differences in susceptibility values exist at the interface between the prostate and rectal-air. This can result in off-resonance magnetic field leading to geometric distortions including signal stretching and signal pile-up in the reconstructed images. Using a set of EPI data acquired with blip-up and blip-down phase encoding gradient directions, model based reconstruction has recently been proposed that can correct these distortions by using a B0 field estimated from a separate B0 scan. However, change in the size of the rectal air region across time can occur that can result in a mismatch of the B0 field to the EPI scan. Also, the measured B0 field itself can be erroneous in regions of low Signal to Noise ratio around the prostate rectal air interface. In this work, using a set of single shot EPI data acquired with blip-up and blip-down phase encoding gradient directions, a novel joint model based reconstruction is proposed that can account for changes in the off resonance effects between the B0 and EPI scans. For ten prostate patients, using a measured B0 field as an initial B0 estimate, on a 5-point scale (1-5) image quality scores evaluated by an experienced radiologist, the proposed framework achieved scores of 3.50 ± 0.85 and 3.40 ± 0.51 for b-values of 0 and 500 s/mm2, respectively compared to 3.40 ± 0.70 and 3.30 ± 0.67 for model based reconstruction. The proposed framework is also capable of estimating a distortion corrected EPI image even without an initial B0 field estimate in situations where a separate B0 scan cannot be obtained due to time constraint.
Collapse
Affiliation(s)
| | | | | | - Alex Kirkham
- University College Hospital, London, United Kingdom
| | | | | |
Collapse
|
5
|
Lee BY, Zhu XH, Chen W. Quantitative analysis of spatial averaging effect on chemical shift imaging SNR and noise coherence with k-space sampling schemes. Magn Reson Imaging 2019; 60:85-92. [PMID: 30943436 DOI: 10.1016/j.mri.2019.03.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 03/25/2019] [Accepted: 03/27/2019] [Indexed: 01/19/2023]
Abstract
Spatial averaging of multiple voxels from high-resolution chemical shift imaging (hrCSI) is a common strategy for in vivo metabolic studies to achieve a better signal-to-noise ratio (SNR) for a region-of-interest. However, the mechanism about how the spatial averaging approach influences the respective spectral signal and noise and its relevance to the k-space sampling schemes remains unclear. Using three-dimension 17O CSI technique with the weighted k-space sampling method of Fourier series window, we performed quantitative SNR comparisons between a single low-resolution CSI (lrCSI) voxel (being 27 times larger than the hrCSI voxel size) and the spatially averaged hrCSI voxels with matched sampling volume and location. We demonstrated that the averaged hrCSI voxel spectrum had a large SNR loss (> 4 times) compared to the lrCSI voxel, which was resulted from unmatched increases in signal (~1.9 fold) and noise (~9.3 fold). The signal increase was caused by the spatial overlapping between the adjacent hrCSI voxels. The substantial noise increase was mainly attributed to the strong noise coherence among hrCSI voxels acquired with the weighted k-space sampling. This study presents a quantitative relation between the k-space sampling schemes to an apparent SNR penalty of the spatial averaging approach. The information could be useful for designing CSI acquisition method and determination of optimal spatial resolution for in vivo metabolic imaging studies.
Collapse
Affiliation(s)
- Byeong-Yeul Lee
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota Medical School, MN, USA.
| | - Xiao-Hong Zhu
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota Medical School, MN, USA
| | - Wei Chen
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota Medical School, MN, USA.
| |
Collapse
|
6
|
Usman M, Kakkar L, Kirkham A, Arridge S, Atkinson D. Model-based reconstruction framework for correction of signal pile-up and geometric distortions in prostate diffusion MRI. Magn Reson Med 2019; 81:1979-1992. [PMID: 30393895 PMCID: PMC6492108 DOI: 10.1002/mrm.27547] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 08/20/2018] [Accepted: 09/03/2018] [Indexed: 12/30/2022]
Abstract
PURPOSE Prostate diffusion-weighted MRI scans can suffer from geometric distortions, signal pileup, and signal dropout attributed to differences in tissue susceptibility values at the interface between the prostate and rectal air. The aim of this work is to present and validate a novel model based reconstruction method that can correct for these distortions. METHODS In regions of severe signal pileup, standard techniques for distortion correction have difficulty recovering the underlying true signal. Furthermore, because of drifts and inaccuracies in the determination of center frequency, echo planar imaging (EPI) scans can be shifted in the phase-encoding direction. In this work, using a B0 field map and a set of EPI data acquired with blip-up and blip-down phase encoding gradients, we model the distortion correction problem linking the distortion-free image to the acquired raw corrupted k-space data and solve it in a manner analogous to the sensitivity encoding method. Both a quantitative and qualitative assessment of the proposed method is performed in vivo in 10 patients. RESULTS Without distortion correction, mean Dice similarity scores between a reference T2W and the uncorrected EPI images were 0.64 and 0.60 for b-values of 0 and 500 s/mm2 , respectively. Compared to the Topup (distortion correction method commonly used for neuro imaging), the proposed method achieved Dice scores (0.87 and 0.85 versus 0.82 and 0.80) and better qualitative results in patients where signal pileup was present because of high rectal gas residue. CONCLUSION Model-based reconstruction can be used for distortion correction in prostate diffusion MRI.
Collapse
Affiliation(s)
- Muhammad Usman
- Centre for Medical Image Computing, Department of Computer ScienceUniversity College LondonLondonUnited Kingdom
| | - Lebina Kakkar
- Centre for Medical Imaging, Division of MedicineUniversity College HospitalLondonUnited Kingdom
| | - Alex Kirkham
- Department of RadiologyUniversity College HospitalLondonUnited Kingdom
| | - Simon Arridge
- Centre for Medical Image Computing, Department of Computer ScienceUniversity College LondonLondonUnited Kingdom
| | - David Atkinson
- Centre for Medical Imaging, Division of MedicineUniversity College HospitalLondonUnited Kingdom
| |
Collapse
|
7
|
de Guzman AE, Wong MD, Gleave JA, Nieman BJ. Variations in post-perfusion immersion fixation and storage alter MRI measurements of mouse brain morphometry. Neuroimage 2016; 142:687-695. [DOI: 10.1016/j.neuroimage.2016.06.028] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 05/20/2016] [Accepted: 06/16/2016] [Indexed: 11/15/2022] Open
|
8
|
Powell NM, Modat M, Cardoso MJ, Ma D, Holmes HE, Yu Y, O’Callaghan J, Cleary JO, Sinclair B, Wiseman FK, Tybulewicz VLJ, Fisher EMC, Lythgoe MF, Ourselin S. Fully-Automated μMRI Morphometric Phenotyping of the Tc1 Mouse Model of Down Syndrome. PLoS One 2016; 11:e0162974. [PMID: 27658297 PMCID: PMC5033246 DOI: 10.1371/journal.pone.0162974] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 08/31/2016] [Indexed: 01/07/2023] Open
Abstract
We describe a fully automated pipeline for the morphometric phenotyping of mouse brains from μMRI data, and show its application to the Tc1 mouse model of Down syndrome, to identify new morphological phenotypes in the brain of this first transchromosomic animal carrying human chromosome 21. We incorporate an accessible approach for simultaneously scanning multiple ex vivo brains, requiring only a 3D-printed brain holder, and novel image processing steps for their separation and orientation. We employ clinically established multi-atlas techniques–superior to single-atlas methods–together with publicly-available atlas databases for automatic skull-stripping and tissue segmentation, providing high-quality, subject-specific tissue maps. We follow these steps with group-wise registration, structural parcellation and both Voxel- and Tensor-Based Morphometry–advantageous for their ability to highlight morphological differences without the laborious delineation of regions of interest. We show the application of freely available open-source software developed for clinical MRI analysis to mouse brain data: NiftySeg for segmentation and NiftyReg for registration, and discuss atlases and parameters suitable for the preclinical paradigm. We used this pipeline to compare 29 Tc1 brains with 26 wild-type littermate controls, imaged ex vivo at 9.4T. We show an unexpected increase in Tc1 total intracranial volume and, controlling for this, local volume and grey matter density reductions in the Tc1 brain compared to the wild-types, most prominently in the cerebellum, in agreement with human DS and previous histological findings.
Collapse
Affiliation(s)
- Nick M. Powell
- Translational Imaging Group, Centre for Medical Image Computing, University College London, 3rd Floor, Wolfson House, 4 Stephenson Way, London NW1 2HE, United Kingdom
- Centre for Advanced Biomedical Imaging, Division of Medicine, University College London, Paul O’Gorman Building, 72 Huntley Street, London WC1E 6DD, United Kingdom
- * E-mail:
| | - Marc Modat
- Translational Imaging Group, Centre for Medical Image Computing, University College London, 3rd Floor, Wolfson House, 4 Stephenson Way, London NW1 2HE, United Kingdom
| | - M. Jorge Cardoso
- Translational Imaging Group, Centre for Medical Image Computing, University College London, 3rd Floor, Wolfson House, 4 Stephenson Way, London NW1 2HE, United Kingdom
| | - Da Ma
- Translational Imaging Group, Centre for Medical Image Computing, University College London, 3rd Floor, Wolfson House, 4 Stephenson Way, London NW1 2HE, United Kingdom
- Centre for Advanced Biomedical Imaging, Division of Medicine, University College London, Paul O’Gorman Building, 72 Huntley Street, London WC1E 6DD, United Kingdom
| | - Holly E. Holmes
- Centre for Advanced Biomedical Imaging, Division of Medicine, University College London, Paul O’Gorman Building, 72 Huntley Street, London WC1E 6DD, United Kingdom
| | - Yichao Yu
- Centre for Advanced Biomedical Imaging, Division of Medicine, University College London, Paul O’Gorman Building, 72 Huntley Street, London WC1E 6DD, United Kingdom
| | - James O’Callaghan
- Centre for Advanced Biomedical Imaging, Division of Medicine, University College London, Paul O’Gorman Building, 72 Huntley Street, London WC1E 6DD, United Kingdom
| | - Jon O. Cleary
- Centre for Advanced Biomedical Imaging, Division of Medicine, University College London, Paul O’Gorman Building, 72 Huntley Street, London WC1E 6DD, United Kingdom
- Melbourne Brain Centre Imaging Unit, Department of Anatomy and Neuroscience, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Ben Sinclair
- Centre for Advanced Biomedical Imaging, Division of Medicine, University College London, Paul O’Gorman Building, 72 Huntley Street, London WC1E 6DD, United Kingdom
| | - Frances K. Wiseman
- Department of Neurodegenerative Disease, Institute of Neurology, University College, London WC1N 3BG, United Kingdom
| | - Victor L. J. Tybulewicz
- The Francis Crick Institute, Mill Hill Laboratory, London NW7 1AA, United Kingdom
- Imperial College, London W12 0NN, United Kingdom
| | - Elizabeth M. C. Fisher
- Department of Neurodegenerative Disease, Institute of Neurology, University College, London WC1N 3BG, United Kingdom
| | - Mark F. Lythgoe
- Centre for Advanced Biomedical Imaging, Division of Medicine, University College London, Paul O’Gorman Building, 72 Huntley Street, London WC1E 6DD, United Kingdom
| | - Sébastien Ourselin
- Translational Imaging Group, Centre for Medical Image Computing, University College London, 3rd Floor, Wolfson House, 4 Stephenson Way, London NW1 2HE, United Kingdom
| |
Collapse
|
9
|
Sasaki K, Sumiyoshi A, Nonaka H, Kasahara Y, Ikeda K, Hall FS, Uhl GR, Watanabe M, Kawashima R, Sora I. Specific regions display altered grey matter volume in μ-opioid receptor knockout mice: MRI voxel-based morphometry. Br J Pharmacol 2014; 172:654-67. [PMID: 24913308 DOI: 10.1111/bph.12807] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 05/09/2014] [Accepted: 05/24/2014] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND AND PURPOSE μ Opioid receptor knockout (MOP-KO) mice display several behavioural differences from wild-type (WT) littermates including differential responses to nociceptive stimuli. Brain structural changes have been tied to behavioural alterations noted in transgenic mice with targeting of different genes. Hence, we assess the brain structure of MOP-KO mice. EXPERIMENTAL APPROACH Magnetic resonance imaging (MRI) voxel-based morphometry (VBM) and histological methods were used to identify structural differences between extensively backcrossed MOP-KO mice and WT mice. KEY RESULTS MOP-KO mice displayed robust increases in regional grey matter volume in olfactory bulb, several hypothalamic nuclei, periaqueductal grey (PAG) and several cerebellar areas, most confirmed by VBM analysis. The largest increases in grey matter volume were detected in the glomerular layer of the olfactory bulb, arcuate nucleus of hypothalamus, ventrolateral PAG (VLPAG) and cerebellar regions including paramedian and cerebellar lobules. Histological analyses confirm several of these results, with increased VLPAG cell numbers and increased thickness of the olfactory bulb granule cell layer and cerebellar molecular and granular cell layers. CONCLUSIONS AND IMPLICATIONS MOP deletion causes previously undescribed structural changes in specific brain regions, but not in all regions with high MOP receptor densities (e.g. thalamus, nucleus accumbens) or that exhibit adult neurogenesis (e.g. hippocampus). Volume differences in hypothalamus and PAG may reflect behavioural changes including hyperalgesia. Although the precise relationship between volume change and MOP receptor deletion was not determined from this study alone, these findings suggest that levels of MOP receptor expression may influence a broader range of neural structure and function in humans than previously supposed. LINKED ARTICLES This article is part of a themed section on Opioids: New Pathways to Functional Selectivity. To view the other articles in this section visit http://dx.doi.org/10.1111/bph.2015.172.issue-2.
Collapse
Affiliation(s)
- Kazumasu Sasaki
- Department of Biological Psychiatry, Tohoku University Graduate School of Medicine, Sendai, Japan; Department of Functional Brain Imaging, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | | | | | | | | | | | | | | | | | | |
Collapse
|
10
|
Sumiyoshi A, Taki Y, Nonaka H, Takeuchi H, Kawashima R. Regional gray matter volume increases following 7days of voluntary wheel running exercise: a longitudinal VBM study in rats. Neuroimage 2014; 98:82-90. [PMID: 24816532 DOI: 10.1016/j.neuroimage.2014.04.075] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 04/22/2014] [Accepted: 04/28/2014] [Indexed: 02/08/2023] Open
Abstract
The effects of physical exercise on brain morphology in rodents have been well documented in histological studies. However, to further understand when and where morphological changes occur in the whole brain, a noninvasive neuroimaging method allowing an unbiased, comprehensive, and longitudinal investigation of brain morphology should be used. In this study, we investigated the effects of 7days of voluntary wheel running exercise on regional gray matter volume (rGMV) using longitudinal voxel-based morphometry (VBM) in rats. Eighteen pairs of adult male naïve Wistar rats were randomized to the exercise or control condition (one rat for each condition from each pair). Each rat was scanned in a 7.0-T MRI scanner at three time points: before exercise, after 7days of exercise, and after 7days of follow-up. The T2-weighted MRI images were segmented using the rat brain tissue priors that were recently published by our laboratory, and the intra- and inter-subject template creation steps were followed. Longitudinal VBM analysis revealed significant increases in rGMV in the motor, somatosensory, association, and visual cortices in the exercise group. Among these brain regions, rGMV changes in the motor cortex were positively correlated with the total distance that was run during the 7days of exercise. In addition, the effects of 7days of exercise on rGMV persisted after 7days of follow-up. These results support the utility of a longitudinal VBM study in rats and provide new insights into experience-dependent structural brain plasticity in naïve adult animals.
Collapse
Affiliation(s)
- Akira Sumiyoshi
- Department of Functional Brain Imaging, Institute of Development, Aging and Cancer, Tohoku University, Sendai 980-8575, Japan.
| | - Yasuyuki Taki
- Division of Developmental Cognitive Neuroscience, Institute of Development, Aging and Cancer, Tohoku University, Sendai 980-8575, Japan; Department of Radiology and Nuclear Medicine, Institute of Development, Aging and Cancer, Tohoku University, Sendai 980-8575, Japan; Division of Medical Image Analysis, Department of Community Medical Supports, Tohoku Medical Megabank Organization, Tohoku University, Sendai 980-8575, Japan
| | - Hiroi Nonaka
- Department of Functional Brain Imaging, Institute of Development, Aging and Cancer, Tohoku University, Sendai 980-8575, Japan
| | - Hikaru Takeuchi
- Division of Developmental Cognitive Neuroscience, Institute of Development, Aging and Cancer, Tohoku University, Sendai 980-8575, Japan
| | - Ryuta Kawashima
- Department of Functional Brain Imaging, Institute of Development, Aging and Cancer, Tohoku University, Sendai 980-8575, Japan; Division of Developmental Cognitive Neuroscience, Institute of Development, Aging and Cancer, Tohoku University, Sendai 980-8575, Japan; Smart Ageing International Research Center, Institute of Development, Aging and Cancer, Tohoku University, Sendai 980-8575, Japan
| |
Collapse
|
11
|
van Eede MC, Scholz J, Chakravarty MM, Henkelman RM, Lerch JP. Mapping registration sensitivity in MR mouse brain images. Neuroimage 2013; 82:226-36. [PMID: 23756204 DOI: 10.1016/j.neuroimage.2013.06.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 05/28/2013] [Accepted: 06/01/2013] [Indexed: 01/15/2023] Open
Abstract
Nonlinear registration algorithms provide a way to estimate structural (brain) differences based on magnetic resonance images. Their ability to align images of different individuals and across modalities has been well-researched, but the bounds of their sensitivity with respect to the recovery of salient morphological differences between groups are unclear. Here we develop a novel approach to simulate deformations on MR brain images to evaluate the ability of two registration algorithms to extract structural differences corresponding to biologically plausible atrophy and expansion. We show that at a neuroanatomical level registration accuracy is influenced by the size and compactness of structures, but do so differently depending on how much change is simulated. The size of structures has a small influence on the recovered accuracy. There is a trend for larger structures to be recovered more accurately, which becomes only significant as the amount of simulated change is large. More compact structures can be recovered more accurately regardless of the amount of simulated change. Both tested algorithms underestimate the full extent of the simulated atrophy and expansion. Finally we show that when multiple comparisons are corrected for at a voxelwise level, a very low rate of false positives is obtained. More interesting is that true positive rates average around 40%, indicating that the simulated changes are not fully recovered. Simulation experiments were run using two fundamentally different registration algorithms and we identified the same results, suggesting that our findings are generalizable across different classes of nonlinear registration algorithms.
Collapse
Affiliation(s)
- Matthijs C van Eede
- Mouse Imaging Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.
| | | | | | | | | |
Collapse
|
12
|
Scheenstra A, Dijkstra J, van der Weerd L. Volumetry and other quantitative measurements to assess the rodent brain. Methods Mol Biol 2012; 771:277-91. [PMID: 21874484 DOI: 10.1007/978-1-61779-219-9_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Morphometry is defined as studying variations in and changes of shapes. Evaluation of shape changes in the brain is a key step in the development of new mouse models, the monitoring of different pathologies, and measuring environmental influences. Traditional morphometry was performed by manual shape delineation, so-called volumetry. Currently, automated methods have been developed that can be roughly divided into three groups: voxel-based morphometry, deformation-based morphometry, and shape-based morphometry. In this chapter, we describe the different approaches for quantitative morphometry and how they can be applied to the quantitative analysis of the rodent brain.
Collapse
Affiliation(s)
- Alize Scheenstra
- Division of Image Processing, Department of Radiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands.
| | | | | |
Collapse
|
13
|
Possibilities and limitations for high resolution small animal MRI on a clinical whole-body 3T scanner. MAGNETIC RESONANCE MATERIALS IN PHYSICS BIOLOGY AND MEDICINE 2011; 25:233-44. [PMID: 22042538 DOI: 10.1007/s10334-011-0284-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 08/16/2011] [Accepted: 09/13/2011] [Indexed: 01/01/2023]
Abstract
OBJECT To investigate the potential of a clinical 3 T scanner to perform MRI of small rodents. MATERIALS AND METHODS Different dedicated small animal coils and several imaging sequences were evaluated to optimize image quality with respect to SNR, contrast and spatial resolution. As an application, optimal grey-white-matter contrast and resolution were investigated for rats. Furthermore, manganese-enhanced MRI was applied in mice with unilateral crush injury of the optic nerve to investigate coil performance on topographic mapping of the visual projection. RESULTS Differences in SNR and CNR up to factor 3 and more were observed between the investigated coils. The best grey-white matter contrast was achieved with a high resolution 3D T (2)-weighted TSE (SPACE) sequence. Delineation of the retino-tectal projection and detection of defined visual pathway damage on the level of the optic nerve could be achieved by using a T (1)-weighted, 3D gradient echo sequence with isotropic resolution of (0.2 mm)(3). CONCLUSIONS Experimental studies in small rodents requiring high spatial resolution can be performed by using a clinical 3 T scanner with appropriate dedicated coils.
Collapse
|
14
|
Mouse phenotyping with MRI. Methods Mol Biol 2011. [PMID: 21874500 DOI: 10.1007/978-1-61779-219-9_31] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The field of mouse phenotyping with magnetic resonance imaging (MRI) is rapidly growing, motivated by the need for improved tools for characterizing and evaluating mouse models of human disease. Image results can provide important comparisons of human conditions with mouse disease models, evaluations of treatment, development or disease progression, as well as direction for histological or other investigations. Effective mouse MRI studies require attention to many aspects of experiment design. In this chapter, we provide details and discussion of important practical considerations: hardware requirements, mouse handling for in vivo imaging, specimen preparation for ex vivo imaging, sequence and contrast agent selection, study size, and quantitative image analysis. We focus particularly on anatomical phenotyping, an important and accessible application that has shown a high potential for impact in many mouse models at our imaging center.
Collapse
|
15
|
Abstract
The laboratory mouse, with its genetic similarity to humans and rich set of tools for manipulating its genome, has emerged as one of the key models for experimental investigation of the genotype/phenotype relationships in mammals. Recent innovations have made MRI an increasingly popular tool for examining the phenotype of genetically altered mice. Advances in field strengths, mouse handling, image analysis and statistics have contributed greatly in this regard. In this chapter, we illustrate the methods necessary to achieve high-throughput phenotyping of genetically altered mice using multiple-mouse MRI combined with advanced image analysis techniques and statistics.
Collapse
Affiliation(s)
- Jason P Lerch
- The Mouse Imaging Centre, Hospital for Sick Children, Toronto, ON, Canada.
| | | | | |
Collapse
|
16
|
Portnoy S, Kale SC, Feintuch A, Tardif C, Pike GB, Henkelman RM. Information content of SNR/resolution trade-offs in three-dimensional magnetic resonance imaging. Med Phys 2009; 36:1442-51. [PMID: 19472651 DOI: 10.1118/1.3098124] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
In MRI, a trade-off exists between resolution and signal-to-noise ratio, since different fractions of the available scan time can be used to acquire data at higher spatial frequencies and to perform signal averaging. By comparing a wide variety of 3D isotropic MR scans with different combinations of SNR, resolution, and scan duration, the impact of this trade-off on the image information content was assessed. The information content of mouse brain, mouse whole-body, and human brain images was evaluated using a simple numerical approach, which sums the information contribution of each individual k-space data point. Results show that, with a fixed receiver bandwidth and field of view, the information content of trade-off images is always maximized when the SNR is equal to about 16. The optimal imaging resolution is dependent on the scan duration, as well as certain MR system properties, such as field strength and coil sensitivity. These properties are, however, easily accounted for with the acquisition of a single scout MR image, and the optimal imaging resolution can then be calculated using a simple mathematical relationship. If the imaging task is approached with a predetermined resolution requirement, the same scout scan can be used to calculate the scan duration that will provide the maximum possible information. Using these relationships to maximize the image information content is an excellent technique for guiding the initial selection of imaging parameters.
Collapse
Affiliation(s)
- S Portnoy
- Mouse Imaging Centre, Toronto Centre for Phenogenomics, Toronto, Ontario M5T 3H7, Canada.
| | | | | | | | | | | |
Collapse
|
17
|
Kale SC, Chen XJ, Henkelman RM. Trading off SNR and resolution in MR images. NMR IN BIOMEDICINE 2009; 22:488-494. [PMID: 19123210 DOI: 10.1002/nbm.1359] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
With a fixed time to acquire a magnetic resonance (MR) image, time can be spent to acquire better spatial resolution with decrease in signal-to-noise ratio (SNR) or decreased resolution with increase in SNR. This resolution/SNR tradeoff at fixed time has been investigated by a visual rater study using images of ex vivo mouse brains. Simulated images with a tradeoff between SNR and resolution were produced from high-quality, 3D isotropic mouse brain images to emulate shorter constant acquisition times. The tradeoff images spanned a range of SNRs (63-6) and isotropic resolutions (32-81 microm). Fourteen readers identified the image which best displayed neuroanatomy. Additional experiments tested for (i) intra-observer consistency, (ii) the effect of emulated scan time, and (iii) specifically biased questions pertaining to the perception of neuroanatomy. Optimal anatomical viewing depended primarily on the SNR of the images. Specifically, for fixed imaging time, preference lay in the SNR range of approximately 30-35 with strong consistency and there was minimal effect from overall imaging time.
Collapse
Affiliation(s)
- Shoan C Kale
- Mouse Imaging Centre, Hospital for Sick Children, Toronto, Ontario, Canada
| | | | | |
Collapse
|
18
|
Dorr AE, Lerch JP, Spring S, Kabani N, Henkelman RM. High resolution three-dimensional brain atlas using an average magnetic resonance image of 40 adult C57Bl/6J mice. Neuroimage 2008; 42:60-9. [PMID: 18502665 DOI: 10.1016/j.neuroimage.2008.03.037] [Citation(s) in RCA: 354] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2007] [Revised: 02/26/2008] [Accepted: 03/16/2008] [Indexed: 10/22/2022] Open
Abstract
Detailed anatomical atlases can provide considerable interpretive power in studies of both human and rodent neuroanatomy. Here we describe a three-dimensional atlas of the mouse brain, manually segmented into 62 structures, based on an average of 32 mum isotropic resolution T(2)-weighted, within skull images of forty 12 week old C57Bl/6J mice, scanned on a 7 T scanner. Individual scans were normalized, registered, and averaged into one volume. Structures within the cerebrum, cerebellum, and brainstem were painted on each slice of the average MR image while using simultaneous viewing of the coronal, sagittal and horizontal orientations. The final product, which will be freely available to the research community, provides the most detailed MR-based, three-dimensional neuroanatomical atlas of the whole brain yet created. The atlas is furthermore accompanied by ancillary detailed descriptions of boundaries for each structure and provides high quality neuroanatomical details pertinent to MR studies using mouse models in research.
Collapse
Affiliation(s)
- A E Dorr
- Clinical Integrative Biology, Sunnybrook Health Sciences Centre, Toronto ON, Canada
| | | | | | | | | |
Collapse
|