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

Objective 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. Materials and 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). Results 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. Conclusion 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.研究目标： 既往研究中，我们基于脑脊液（cerebrospinal fluid, CSF）的长T2弛豫特性开发了一款快速脑脊液MRI序列。通过处理该序列采集的数据，可自动获取脑实质体积（brain parenchymal volume, BPV）与颅内体积（intracranial volume, ICV）。本研究旨在评估该脑脊液MRI序列的脑实质体积与颅内体积测量精度，并通过与基于3D T1的脑部分割方法对比，验证该序列的有效性。 材料与方法： 招募10名健康受试者（2名女性，年龄中位数为28岁），采用3T磁共振成像设备完成两次扫描，两次扫描间对受试者进行重新摆位。本次扫描方案包含：低分辨率（low resolution, LR）脑脊液序列（扫描时长0:57分钟）、高分辨率（high resolution, HR）脑脊液序列（扫描时长3:21分钟）以及3D T1加权序列（扫描时长6:47分钟）。将高分辨率3D T1加权图像的数据进行下采样，以生成低分辨率T1加权图像（重建成像时长：1:59分钟）。采用自研软件对脑脊液MRI序列的数据实施自动分割；采用FSL（5.0）、SPM12及FreeSurfer（5.3.0）对3D T1加权图像进行分割。 研究结果： 两次扫描间，脑脊液低分辨率序列的脑实质体积与颅内体积的平均绝对差异为12±9/7±4 cc，脑脊液高分辨率序列为5±5/4±2 cc，该结果与FSL高分辨率（9±11/19±23 cc）、FSL低分辨率（7±4/6±5 cc）、FreeSurfer高分辨率（5±3/14±8 cc）、FreeSurfer低分辨率（9±8/12±10 cc）、SPM高分辨率（5±3/4±7 cc）及SPM低分辨率（5±4/5±3 cc）的测量结果相当。脑脊液序列的测量体积与FSL、FreeSurfer、SPM的高、低分辨率序列的测量体积之间相关性极佳（所有皮尔逊相关系数均>0.83，决定系数R²为0.67~0.97）。下采样数据与高分辨率数据的结果相似。 研究结论： 两款脑脊液MRI序列的测量精度均与成熟的基于3D T1的自动脑分割方法相当，且与后者的脑实质体积与颅内体积分割结果具有良好的相关性。但该快速脑脊液MRI序列的扫描时长极短，显著优于需采用成熟分割方法的3D T1序列。