Dataset Information

Fast CSF MRI for brain segmentation; Cross-validation by comparison with 3D T1-based brain segmentation methods.

ABSTRACT: In previous work we have developed a fast sequence that focusses on cerebrospinal fluid (CSF) based on the long T2 of CSF. By processing the data obtained with this CSF MRI sequence, brain parenchymal volume (BPV) and intracranial volume (ICV) can be automatically obtained. The aim of this study was to assess the precision of the BPV and ICV measurements of the CSF MRI sequence and to validate the CSF MRI sequence by comparison with 3D T1-based brain segmentation methods.Ten healthy volunteers (2 females; median age 28 years) were scanned (3T MRI) twice with repositioning in between. The scan protocol consisted of a low resolution (LR) CSF sequence (0:57min), a high resolution (HR) CSF sequence (3:21min) and a 3D T1-weighted sequence (6:47min). Data of the HR 3D-T1-weighted images were downsampled to obtain LR T1-weighted images (reconstructed imaging time: 1:59 min). Data of the CSF MRI sequences was automatically segmented using in-house software. The 3D T1-weighted images were segmented using FSL (5.0), SPM12 and FreeSurfer (5.3.0).The mean absolute differences for BPV and ICV between the first and second scan for CSF LR (BPV/ICV: 12±9/7±4cc) and CSF HR (5±5/4±2cc) were comparable to FSL HR (9±11/19±23cc), FSL LR (7±4, 6±5cc), FreeSurfer HR (5±3/14±8cc), FreeSurfer LR (9±8, 12±10cc), and SPM HR (5±3/4±7cc), and SPM LR (5±4, 5±3cc). The correlation between the measured volumes of the CSF sequences and that measured by FSL, FreeSurfer and SPM HR and LR was very good (all Pearson's correlation coefficients >0.83, R2 .67-.97). The results from the downsampled data and the high-resolution data were similar.Both CSF MRI sequences have a precision comparable to, and a very good correlation with established 3D T1-based automated segmentations methods for the segmentation of BPV and ICV. However, the short imaging time of the fast CSF MRI sequence is superior to the 3D T1 sequence on which segmentation with established methods is performed.

SUBMITTER: van der Kleij LA

PROVIDER: S-EPMC5908081 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Fast CSF MRI for brain segmentation; Cross-validation by comparison with 3D T1-based brain segmentation methods.

van der Kleij Lisa A LA de Bresser Jeroen J Hendrikse Jeroen J Siero Jeroen C W JCW Petersen Esben T ET De Vis Jill B JB

PloS one 20180419 4

<h4>Objective</h4>In previous work we have developed a fast sequence that focusses on cerebrospinal fluid (CSF) based on the long T2 of CSF. By processing the data obtained with this CSF MRI sequence, brain parenchymal volume (BPV) and intracranial volume (ICV) can be automatically obtained. The aim of this study was to assess the precision of the BPV and ICV measurements of the CSF MRI sequence and to validate the CSF MRI sequence by comparison with 3D T1-based brain segmentation methods.<h4>Ma ...[more]

PMID: 29672584

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Project description:Background and purposeLimited evidence has suggested that a deep learning automatic brain segmentation and classification method, based on T1-weighted brain MR images, can predict Alzheimer disease. Our aim was to develop and validate a deep learning-based automatic brain segmentation and classification algorithm for the diagnosis of Alzheimer disease using 3D T1-weighted brain MR images.Materials and methodsA deep learning-based algorithm was developed using a dataset of T1-weighted brain MR images in consecutive patients with Alzheimer disease and mild cognitive impairment. We developed a 2-step algorithm using a convolutional neural network to perform brain parcellation followed by 3 classifier techniques including XGBoost for disease prediction. All classification experiments were performed using 5-fold cross-validation. The diagnostic performance of the XGBoost method was compared with logistic regression and a linear Support Vector Machine by calculating their areas under the curve for differentiating Alzheimer disease from mild cognitive impairment and mild cognitive impairment from healthy controls.ResultsIn a total of 4 datasets, 1099, 212, 711, and 705 eligible patients were included. Compared with the linear Support Vector Machine and logistic regression, XGBoost significantly improved the prediction of Alzheimer disease (P < .001). In terms of differentiating Alzheimer disease from mild cognitive impairment, the 3 algorithms resulted in areas under the curve of 0.758-0.825. XGBoost had a sensitivity of 68% and a specificity of 70%. In terms of differentiating mild cognitive impairment from the healthy control group, the 3 algorithms resulted in areas under the curve of 0.668-0.870. XGBoost had a sensitivity of 79% and a specificity of 80%.ConclusionsThe deep learning-based automatic brain segmentation and classification algorithm allowed an accurate diagnosis of Alzheimer disease using T1-weighted brain MR images. The widespread availability of T1-weighted brain MR imaging suggests that this algorithm is a promising and widely applicable method for predicting Alzheimer disease.

Project description:Vessel wall imaging techniques have been introduced to assess the burden of peripheral arterial disease (PAD) in terms of vessel wall thickness, area or volume. Recent advances in a 3D black-blood MRI sequence known as the 3D motion-sensitized driven equilibrium (MSDE) prepared rapid gradient echo sequence (3D MERGE) have allowed the acquisition of vessel wall images with up to 50 cm coverage, facilitating noninvasive and detailed assessment of PAD. This work introduces an algorithm that combines 2D slice-based segmentation and 3D user editing to allow for efficient plaque burden analysis of the femoral artery images acquired using 3D MERGE.The 2D slice-based segmentation approach is based on propagating segmentation results of contiguous 2D slices. The 3D image volume was then reformatted using the curved planar reformation (CPR) technique. User editing of the segmented contours was performed on the CPR views taken at different angles. The method was evaluated on six femoral artery images. Vessel wall thickness and area obtained before and after editing on the CPR views were assessed by comparison with manual segmentation. Difference between semiautomatically and manually segmented contours were compared with the difference of the corresponding measurements between two repeated manual segmentations.The root-mean-square (RMS) errors of the mean wall thickness (t(mean)) and the wall area (WA) of the edited contours were 0.35 mm and 7.1 mm(2), respectively, which are close to the RMS difference between two repeated manual segmentations (RMSE: 0.33 mm in t(mean), 6.6 mm(2) in WA). The time required for the entire semiautomated segmentation process was only 1%-2% of the time required for manual segmentation.The difference between the boundaries generated by the proposed algorithm and the manually segmented boundary is close to the difference between repeated manual segmentations. The proposed method provides accurate plaque burden measurements, while considerably reducing the analysis time compared to manual review.

Dataset Information

Fast CSF MRI for brain segmentation; Cross-validation by comparison with 3D T1-based brain segmentation methods.

Publications

Fast CSF MRI for brain segmentation; Cross-validation by comparison with 3D T1-based brain segmentation methods.

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