This study protocol adhered to the ethical principles outlined in the Declaration of Helsinki and was approved by the Shenzhen Bao'an District Songgang People's Hospital ethics review board (Approval number: IRB-YJ-2025-045). Given its retrospective design, the study involved only the analysis of archived clinical and imaging data. All patient-identifiable information was strictly anonymized.
Research design and subjects
This study is a retrospective diagnostic analysis. We retrospectively collected clinical and imaging data from brain tumor patients admitted to the Neurosurgical Oncology Departments of Songgang People's Hospital, Bao'an District, Shenzhen, and Shenzhen Second People's Hospital between January 2024 and June 2025. All patients had pathologically confirmed diagnoses post-surgery. A total of 105 patients were finally included, all of whom underwent both conventional MRI and APT imaging examinations preoperatively. According to the 2021 WHO Classification of Tumors of the Central Nervous System32, the patients were divided into three groups: Meningioma Group: 55 cases, pathologically confirmed as WHO grades I-II. Low-Grade Glioma (LGG) Group: 20 cases, pathologically confirmed as WHO grades I-II. HGG Group: 30 cases, pathologically confirmed as WHO grades III-IV. All patients underwent both conventional MRI and APT imaging examinations preoperatively. The detailed study flowchart is presented in Figure 1.
Inclusion and exclusion criteria
Inclusion criteria were (1) patients undergoing initial surgical resection with a definitive histopathological diagnosis of meningioma (WHO grades I-II), LGGs (WHO grades I-II), or HGGs (WHO grades III-IV); (2) completion of non-contrast head MRI, T1-weighted contrast-enhanced scanning, and APT imaging within one week prior to surgery; (3) availability of complete imaging data with good image quality, free from significant artifacts, suitable for diagnostic evaluation and measurements; (4) availability of complete clinical data and follow-up records.
Exclusion criteria were (1) patients who had received any anti-tumor therapy (e.g., radiotherapy, chemotherapy, targeted therapy, or immunotherapy) prior to surgery; (2) patients with recurrent brain tumors or the presence of other intracranial space-occupying lesions; (3) patients with contraindications to MRI examination; (4) images with severe motion artifacts or susceptibility artifacts that would affect subsequent data analysis; (5) pathological diagnosis of central nervous system tumor types other than those specified above.
Sample size calculation
This study was a retrospective diagnostic analysis, and the sample size was primarily determined by all available cases that met the inclusion criteria during the study period. To evaluate whether the current sample size was sufficient to detect statistically significant differences in APT parameters between groups, we referred to differences in APT signal values between different-grade gliomas and meningiomas reported in previous literature33. Setting α = 0.05 and a statistical power of 0.80, and using a two-sample mean comparison formula for estimation, we determined that a minimum of 15 samples per group was required. Based on the final inclusion of 105 patients (55 meningiomas, 20 LGGs, 30 HGGs), a post-hoc power analysis showed that the power to detect differences in APTmean among the three groups exceeded 0.95 with the current sample size. This indicates that the study sample size was adequate to support statistical inference.
Image acquisition and post processing
MRI scanning protocol:
All patients were scanned using a magnetic resonance (MR) scanner with a standard 8-channel head coil 34. The scanning sequences and parameters were as follows:
Conventional sequences: Axial T1-weighted imaging (T1WI) was performed using a three-dimensional spoiled gradient-echo sequence (3D T1-SPGR, repetition time/echo time [TR/TE] = 8.5/3.4 ms, flip angle = 12°, slice thickness = 1.2 mm, interslice gap = 0 mm, field of view [FOV] = 24 cm × 24 cm, matrix = 256 × 256). Axial T2-weighted imaging (T2WI) was acquired with a fast spin-echo sequence (TR/TE = 4,500/102 ms, slice thickness = 5 mm, interslice gap = 1.5 mm, FOV = 24 cm × 24 cm, matrix = 384 × 224). Fluid-attenuated inversion recovery (FLAIR) images were obtained with repetition time/echo time/inversion time (TR/TE/TI) = 9,000/120/2,250 ms.
Contrast-enhanced scanning: After intravenous bolus injection of gadopentetate dimeglumine at a standard dose of 0.1 mmol/kg body weight and a flow rate of 2 mL/s, followed by a 20 mL saline flush, axial, sagittal, and coronal contrast-enhanced T1WI images were acquired using the same parameters as the precontrast 3D T1-SPGR sequence.
APT imaging sequence: APT imaging was performed using a two-dimensional gradient-echo pulse sequence with the following parameters: TR/TE = 3,000/3.5 ms, slice thickness = 5 mm, FOV = 24 cm × 24 cm, matrix = 128 × 128, number of excitations = 2, and a total acquisition time of 4 min and 32 s. A continuous-wave saturation pulse with a duration of 2 s and a power (B₁) of 2 µT was applied at frequency offsets ranging from −6 to +6 parts per million (ppm) (in steps of 0.5 ppm), including the water resonance frequency at 0 ppm. Under the main magnetic field (B₀), the saturation pulse was specifically applied at the downfield resonance frequency of +3.5 ppm relative to the water proton resonance (0 ppm), corresponding to the amide proton chemical exchange rate. Prior to APT acquisition, B₀ inhomogeneity was corrected using a water saturation shift referencing (WASSR) approach with saturation parameters identical to the main APT scan but at a reduced B₁ amplitude of 0.5 µT. After scanning, APT-weighted images and magnetization transfer ratio asymmetry (MTRasym) maps at 3.5 ppm were automatically generated by the scanner's built-in software by calculating the asymmetry of the magnetization transfer ratio: MTRasym(3.5 ppm)=[S(−3.5 ppm) − S(+3.5 ppm)] / S(0 ppm) where S(Δω) represents the signal intensity with the saturation pulse applied at the indicated frequency offset Δω relative to the water resonance. The positive MTRasym value at 3.5 ppm primarily reflects the amide proton transfer effect, as the magnetization transfer (MT) and nuclear Overhauser effects are approximately symmetric about the water resonance and thus canceled out by the asymmetry calculation.
Image analysis:
All imaging data were independently analyzed by two neuroradiologists with over 5 years of experience using an image-viewing software workstation. Region of Interest (ROI) delineation was performed according to the following standardized procedures:
Tumor solid region: On the contrast-enhanced T1WI images, an ROI was manually drawn along the enhancing margin of the tumor, carefully avoiding necrotic, cystic, and peritumoral edema areas. The ROI was drawn to encompass the entire solid enhancing component on the slice with the maximum tumor diameter.
T2 Hyperintense region: On the T2WI images, an ROI was manually drawn to encompass the entire hyperintense area, including both the tumor and the surrounding peritumoral edema. The boundary was defined as the visible margin at which the hyperintensity met the normal-appearing brain parenchyma.
APT Abnormal signal region: On the APT-weighted MTRasym maps, using the contralateral normal-appearing white matter as a reference, an ROI was manually drawn to include all areas with signal intensity higher than the mean signal of the reference normal tissue plus 2 standard deviations. This threshold-based approach was applied to the same slice as the maximum tumor diameter. The contralateral reference ROI was placed in the centrum semiovale at a mirror location to the tumor, with an area of approximately 100 mm2.
For consistency, each ROI was measured three times on consecutive slices centered at the maximum tumor diameter, and the average value was recorded for analysis. All ROI delineations were performed independently by the two reviewers, and any discrepancies were resolved by consensus. Interobserver agreement was assessed using the intraclass correlation coefficient (ICC), with an ICC > 0.80 indicating excellent agreement.
The following parameters were measured and calculated:
Mean APT Signal Intensity (APTmean): The average MTRasym value at 3.5 ppm within the ROI of the tumor solid region.
Regional ratio calculation:
RAPT/T2: The ratio of the area of the APT abnormal signal region to the area of the T2WI hyperintense region (RAPT / RT2).
RAPT/E: The ratio of the area of the APT abnormal signal region to the area of the T1WI contrast-enhancing region (RAPT / RE).
Clinical outcome measures
The primary evaluation measures of this study were imaging parameters and their diagnostic efficacy, rather than therapeutic clinical outcomes. Primary Imaging Outcomes: APTmean values for each group (meningioma, LGGs, HGG), and the RAPT/T2 and RAPT/E ratios for the LGG and HGG groups.
Statistical analysis
Continuous variables were tested for normality using the Shapiro-Wilk test. Normally distributed data are presented as mean ± standard deviation (SD) and compared with one-way analysis of variance (ANOVA) (Bonferroni post-hoc). Non-normal data and ordinal data are presented as M (Q₁, Q₃) and compared using the Kruskal-Wallis H test (Dunn's test with Bonferroni correction). Categorical data are presented as n (%) and compared using the Chi-square or Fisher’s exact test. ROC curves were plotted to evaluate diagnostic performance. All tests were two-sided; P < 0.05 was considered significant.