DOI: 10.1002/jmri.28937 ISSN: 1053-1807

A Fully Automatic Method to Segment Choroid Plexuses in Multiple Sclerosis Using Conventional MRI Sequences

Loredana Storelli, Elisabetta Pagani, Martina Rubin, Monica Margoni, Massimo Filippi, Maria A. Rocca
  • Radiology, Nuclear Medicine and imaging


Choroid plexus (CP) volume has been recently proposed as a proxy for brain neuroinflammation in multiple sclerosis (MS).


To develop and validate a fast automatic method to segment CP using routinely acquired brain T1‐weighted and FLAIR MRI.

Study Type



Fifty‐five MS patients (33 relapsing–remitting, 22 progressive; mean age = 46.8 ± 10.2 years; 31 women) and 60 healthy controls (HC; mean age = 36.1 ± 12.6 years, 33 women).

Field Strength/Sequence

3D T2‐weighted FLAIR and 3D T1‐weighted gradient echo sequences at 3.0 T.


Brain tissues were segmented on T1‐weighted sequences and a Gaussian Mixture Model (GMM) was fitted to FLAIR image intensities obtained from the ventricle masks of the SIENAX. A second GMM was then applied on the thresholded and filtered ventricle mask. CP volumes were automatically determined and compared with those from manual segmentation by two raters (with 3 and 10 years' experience; reference standard). CP volumes from previously published automatic segmentation methods (freely available Freesurfer [FS] and FS‐GMM) were also compared with reference standard. Expanded Disability Status Scale (EDSS) score was assessed within 3 days of MRI. Computational time was assessed for each automatic technique and manual segmentation.

Statistical Tests

Comparisons of CP volumes with reference standard were evaluated with Bland Altman analysis. Dice similarity coefficients (DSC) were computed to assess automatic CP segmentations. Volume differences between MS and HC for each method were assessed with t‐tests and correlations of CP volumes with EDSS were assessed with Pearson's correlation coefficients (R). A P value <0.05 was considered statistically significant.


Compared to manual segmentation, the proposed method had the highest segmentation accuracy (mean DSC = 0.65 ± 0.06) compared to FS (mean DSC = 0.37 ± 0.08) and FS‐GMM (0.58 ± 0.06). The percentage CP volume differences relative to manual segmentation were −0.1% ± 0.23, 4.6% ± 2.5, and −0.48% ± 2 for the proposed method, FS, and FS‐GMM, respectively. The Pearson's correlations between automatically obtained CP volumes and the manually obtained volumes were 0.70, 0.54, and 0.56 for the proposed method, FS, and FS‐GMM, respectively. A significant correlation between CP volume and EDSS was found for the proposed automatic pipeline (R = 0.2), for FS‐GMM (R = 0.3) and for manual segmentation (R = 0.4). Computational time for the proposed method (32 ± 2 minutes) was similar to the manual segmentation (20 ± 5 minutes) but <25% of the FS (120 ± 15 minutes) and FS‐GMM (125 ± 15 minutes) methods.

Data Conclusion

This study developed an accurate and easily implementable method for automatic CP segmentation in MS using T1‐weighted and FLAIR MRI.

Evidence Level


Technical Efficacy

Stage 4

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