Segmentation of gray matter, white matter, and CSF with fluid and white matter suppression using MP2RAGE

Wang, Yishi; Wang, Yajie; Zhang, Zhe; Xiong, Yuhui; Zhang, Qiang; Yuan, Chun; Guo, Hua

doi:10.1002/jmri.26014

Cited by 19 publications

(15 citation statements)

References 39 publications

(112 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The proposed method allows rapid processing with relevant segmentation of brain tissues. A recent study has reported MP2RAGE-based segmentation using two images with different inversion times, i.e., INV1 and INV2 [28]. The study demonstrated superior segmentation in subcortical structures in comparison with FSL and SPM12, whereas our proposed method produced good segmentation in the cerebellum and WM in the medial part of the brain.…”

Section: Discussionmentioning

confidence: 74%

Brain tissue segmentation based on MP2RAGE multi-contrast images in 7 T MRI

Choi

Kawaguchi²,

Matsuoka

et al. 2018

Preprint

View full text Add to dashboard Cite

We proposed a method for segmentation of brain tissues-gray matter (GM), white matter (WM), and cerebrospinal fluid (CSF)-using multi-contrast images, including a T1 map and a uniform T1-weighted image, from a magnetization-prepared 2 rapid acquisition gradient echoes (MP2RAGE) sequence at 7 Tesla. The proposed method was evaluated with respect to the processing time and the similarity of the segmented masks of brain tissues with those obtained using FreeSurfer, FSL, and SPM12. The processing time of the proposed method (28 ± 0 s) was significantly shorter than those of FSL and SPM12 (444 ± 4 s and 159 ± 2 s for FSL and SPM12, respectively). In the similarity assessment, the tissue mask of the brain obtained by the proposed method showed higher consistency with those obtained by FSL than with those obtained by SPM12. The proposed method misclassified the subcortical structures and large vessels since it is based on the intensities of multi-contrast images obtained using MP2RAGE, which uses a similar segmentation approach as FSL but is not based on a template image or a parcellated brain atlas, which are used for FreeSurfer and SPM12, respectively. However, the proposed method showed good segmentation in the cerebellum and WM in the medial part of the brain in comparison with the other methods. Thus, because the proposed method using different contrast images of MP2RAGE sequence showed the shortest processing time and similar segmentation ability as the other methods, it may be useful for both neuroimaging research and clinical diagnosis.

show abstract

Section: Discussionmentioning

confidence: 74%

Brain tissue segmentation based on MP2RAGE multi-contrast images in 7 T MRI

Choi

Kawaguchi²,

Matsuoka

et al. 2018

Preprint

View full text Add to dashboard Cite

show abstract

“…The proposed method allows rapid processing with relevant segmentation of brain tissues. A recent study has reported MP2RAGE-based segmentation using two images with different inversion times, i.e., INV1 and INV2 [31]. The study demonstrated superior segmentation in subcortical structures in comparison with FSL and SPM12, whereas our proposed method produced good segmentation in the cerebellum and WM in the medial part of the brain.…”

Section: Discussionmentioning

confidence: 81%

Brain tissue segmentation based on MP2RAGE multi-contrast images in 7 T MRI

Choi

Kawaguchi²,

Matsuoka

et al. 2019

PLoS ONE

View full text Add to dashboard Cite

We proposed a method for segmentation of brain tissues—gray matter, white matter, and cerebrospinal fluid—using multi-contrast images, including a T1 map and a uniform T1-weighted image, from a magnetization-prepared 2 rapid acquisition gradient echoes (MP2RAGE) sequence at 7 Tesla. The proposed method was evaluated with respect to the processing time and the similarity of the segmented masks of brain tissues with those obtained using FSL, FreeSurfer, and SPM12. The processing time of the proposed method (28 ± 0 s) was significantly shorter than those of FSL and SPM12 (444 ± 4 s and 159 ± 2 s for FSL and SPM12, respectively). In the similarity assessment, the tissue mask of the brain obtained by the proposed method showed higher consistency with those obtained using FSL than with those obtained using SPM12. The proposed method misclassified the subcortical structures and large vessels since it is based on the intensities of multi-contrast images obtained using MP2RAGE, which uses a similar segmentation approach as FSL but is not based on a template image or a parcellated brain atlas, which are used for FreeSurfer and SPM12, respectively. However, the proposed method showed good segmentation in the cerebellum and white matter in the medial part of the brain in comparison with the other methods. Thus, because the proposed method using different contrast images of MP2RAGE sequence showed the shortest processing time and similar segmentation ability as the other methods, it may be useful for both neuroimaging research and clinical diagnosis.

show abstract

“…We would deploy the sequence in the event we observed pathology on one of the conventional anatomical scans. A future protocol might also include MP2RAGE for tissue and CSF segmentation (Wang et al . 2018), for enhanced deep gray matter contrast (Tanner et al .…”

Section: Discussionmentioning

confidence: 99%

An MRI protocol for anatomical and functional evaluation of the California sea lion brain

Cook

Hoard

Dolui

et al. 2020

Preprint

View full text Add to dashboard Cite

We describe a research MRI protocol for in vivo evaluation of pinniped brains using standard human clinical MRI hardware and pulse sequences. Our intended application is to study development of California sea lions (Zalophus californianus) exposed in utero to domoic acid (DOM) produced by harmful algae blooms in the coastal Pacific Ocean. In cases where the fetus survives to birth, exposure to the toxin in utero could result in developmental abnormalities leading to neurological and behavioral deficits. Prior studies on sea lions naturally exposed to DOM as adults have demonstrated hippocampal atrophy and altered mesial temporal connectivity. This MRI protocol is therefore intended to depict the hippocampal formation as the primary region of interest, and to provide longitudinal measures of brain functional and structural connectivity as well as quantitative anatomical evaluations. Scan quality and utility are assessed by comparison with prior studies in live and post mortem sea lion brains. We include the first determination of cerebral blood flow mapping using MRI, and also the first fiber tractography using diffusion-weighted imaging from a live sea lion brain. The protocol also facilitates screening for common neurological pathologies, including tumors, trauma and hemorrhages. We believe the protocol would be suitable for any pinniped that can fit inside a human MRI scanner.

show abstract

Segmentation of gray matter, white matter, and CSF with fluid and white matter suppression using MP2RAGE

Abstract: 2 Technical Efficacy: Stage 1 J. Magn. Reson. Imaging 2018;48:1540-1550.

Cited by 19 publications

References 39 publications

Brain tissue segmentation based on MP2RAGE multi-contrast images in 7 T MRI

Brain tissue segmentation based on MP2RAGE multi-contrast images in 7 T MRI

Brain tissue segmentation based on MP2RAGE multi-contrast images in 7 T MRI

An MRI protocol for anatomical and functional evaluation of the California sea lion brain

Contact Info

Product

Resources

About