Exploring the Impact of 3D Fast Spin Echo and Inversion Recovery Gradient Echo Sequences Magnetic Resonance Imaging Acquisition on Automated Brain Tumor Segmentation

To conduct a study comparing the performance of automated segmentation techniques using 2 different contrast-enhanced T1-weighted (CET1) magnetic resonance imaging (MRI) acquisition protocol. We collected 100 preoperative glioblastoma (GBM) MRIs consisting of 50 IR-GRE and 50 3-dimensional fast spin...

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Published inMayo Clinic Proceedings. Digital health Vol. 2; no. 2; pp. 231 - 240
Main Authors Moassefi, Mana, Faghani, Shahriar, Khanipour Roshan, Sara, Conte, Gian Marco, Rassoulinejad Mousavi, Seyed Moein, Kaufmann, Timothy J., Erickson, Bradley J.
Format Journal Article
LanguageEnglish
Published Elsevier Inc 01.06.2024
Elsevier
Subjects
CET1
nnUNet
MRI
CEL
TE
3D
GBM
DSC
FLAIR
HD95
FSE
UCSF-PDGM
IR-GRE
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Summary:To conduct a study comparing the performance of automated segmentation techniques using 2 different contrast-enhanced T1-weighted (CET1) magnetic resonance imaging (MRI) acquisition protocol. We collected 100 preoperative glioblastoma (GBM) MRIs consisting of 50 IR-GRE and 50 3-dimensional fast spin echo (3D-FSE) image sets. Their gold-standard tumor segmentation mask was created based on the expert opinion of a neuroradiologist. Cases were randomly divided into training and test sets. We used the no new UNet (nnUNet) architecture pretrained on the 501-image public data set containing IR-GRE sequence image sets, followed by 2 training rounds with the IR-GRE and 3D-FSE images, respectively. For each patient, in the IR-GRE and 3D-FSE test sets, we had 2 prediction masks, one from the model fine-tuned with the IR-GRE training set and one with 3D-FSE. The dice similarity coefficients (DSCs) of the 2 sets of results for each case in the test sets were compared using the Wilcoxon tests. Models trained on 3D-FSE images outperformed IR-GRE models in lesion segmentation, with mean DSC differences of 0.057 and 0.022 in the respective test sets. For the 3D-FSE and IR-GRE test sets, the calculated P values comparing DSCs from 2 models were .02 and .61, respectively. Including 3D-FSE MRI in the training data set improves segmentation performance when segmenting 3D-FSE images.
ISSN:2949-7612
2949-7612
DOI:10.1016/j.mcpdig.2024.03.006