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Park KY, Shimony JS, Chakrabarty S, Tanenbaum AB, Hacker CD, Donovan KM, Luckett PH, Milchenko M, Sotiras A, Marcus DS, Leuthardt EC, Snyder AZ. Optimal approaches to analyzing functional MRI data in glioma patients. J Neurosci Methods 2024; 402:110011. [PMID: 37981126 PMCID: PMC10926951 DOI: 10.1016/j.jneumeth.2023.110011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/18/2023] [Accepted: 11/09/2023] [Indexed: 11/21/2023]
Abstract
BACKGROUND Resting-state fMRI is increasingly used to study the effects of gliomas on the functional organization of the brain. A variety of preprocessing techniques and functional connectivity analyses are represented in the literature. However, there so far has been no systematic comparison of how alternative methods impact observed results. NEW METHOD We first surveyed current literature and identified alternative analytical approaches commonly used in the field. Following, we systematically compared alternative approaches to atlas registration, parcellation scheme, and choice of graph-theoretical measure as regards differentiating glioma patients (N = 59) from age-matched reference subjects (N = 163). RESULTS Our results suggest that non-linear, as opposed to affine registration, improves structural match to an atlas, as well as measures of functional connectivity. Functionally- as opposed to anatomically-derived parcellation schemes maximized the contrast between glioma patients and reference subjects. We also demonstrate that graph-theoretic measures strongly depend on parcellation granularity, parcellation scheme, and graph density. COMPARISON WITH EXISTING METHODS AND CONCLUSIONS Our current work primarily focuses on technical optimization of rs-fMRI analysis in glioma patients and, therefore, is fundamentally different from the bulk of papers discussing glioma-induced functional network changes. We report that the evaluation of glioma-induced alterations in the functional connectome strongly depends on analytical approaches including atlas registration, choice of parcellation scheme, and graph-theoretical measures.
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Affiliation(s)
- Ki Yun Park
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA; Medical Scientist Training Program, Washington University School of Medicine, St. Louis, MO, USA; Division of Neurotechnology, Washington University School of Medicine, St. Louis, MO 63110, USA.
| | - Joshua S Shimony
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Satrajit Chakrabarty
- Department of Electrical and Systems Engineering, Washington University, St. Louis, MO 63130, USA
| | - Aaron B Tanenbaum
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Carl D Hacker
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kara M Donovan
- Department of Biomedical Engineering, Washington University, St. Louis, MO 63130, USA; Division of Neurotechnology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Patrick H Luckett
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA; Division of Neurotechnology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Mikhail Milchenko
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Aristeidis Sotiras
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, MO 63110, USA; Institute for Informatics, Data Science & Biostatistics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Daniel S Marcus
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Eric C Leuthardt
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Biomedical Engineering, Washington University, St. Louis, MO 63130, USA; Department of Mechanical Engineering and Materials Science, Washington University, St. Louis, MO 63130, USA; Center for Innovation in Neuroscience and Technology, Washington University School of Medicine, St. Louis, MO 63110, USA; Brain Laser Center, Washington University School of Medicine, St. Louis, MO 63110, USA; Division of Neurotechnology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Abraham Z Snyder
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
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Guillevin R, Naudin M, Fayolle P, Giraud C, Le Guillou X, Thomas C, Herpe G, Miranville A, Fernandez-Maloigne C, Pellerin L, Guillevin C. Diagnostic and Therapeutic Issues in Glioma Using Imaging Data: The Challenge of Numerical Twinning. J Clin Med 2023; 12:7706. [PMID: 38137775 PMCID: PMC10744312 DOI: 10.3390/jcm12247706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 11/28/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
Glial tumors represent the leading etiology of primary brain tumors. Their particularities lie in (i) their location in a highly functional organ that is difficult to access surgically, including for biopsy, and (ii) their rapid, anisotropic mode of extension, notably via the fiber bundles of the white matter, which further limits the possibilities of resection. The use of mathematical tools enables the development of numerical models representative of the oncotype, genotype, evolution, and therapeutic response of lesions. The significant development of digital technologies linked to high-resolution NMR exploration, coupled with the possibilities offered by AI, means that we can envisage the creation of digital twins of tumors and their host organs, thus reducing the use of physical sampling.
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Affiliation(s)
- Rémy Guillevin
- Department of Imaging, University Hospital Center of Poitiers, 86000 Poitiers, France
- Labcom I3M, University of Poitiers, 86000 Poitiers, France
- DACTIM-MIS Team, Laboratoire de Mathématiques Appliquées LMA, CNRS UMR 7348, 86021 Poitiers, France
| | - Mathieu Naudin
- Department of Imaging, University Hospital Center of Poitiers, 86000 Poitiers, France
- Labcom I3M, University of Poitiers, 86000 Poitiers, France
- DACTIM-MIS Team, Laboratoire de Mathématiques Appliquées LMA, CNRS UMR 7348, 86021 Poitiers, France
| | - Pierre Fayolle
- Department of Imaging, University Hospital Center of Poitiers, 86000 Poitiers, France
- Labcom I3M, University of Poitiers, 86000 Poitiers, France
- DACTIM-MIS Team, Laboratoire de Mathématiques Appliquées LMA, CNRS UMR 7348, 86021 Poitiers, France
| | - Clément Giraud
- Department of Imaging, University Hospital Center of Poitiers, 86000 Poitiers, France
- Labcom I3M, University of Poitiers, 86000 Poitiers, France
- DACTIM-MIS Team, Laboratoire de Mathématiques Appliquées LMA, CNRS UMR 7348, 86021 Poitiers, France
| | - Xavier Le Guillou
- Labcom I3M, University of Poitiers, 86000 Poitiers, France
- DACTIM-MIS Team, Laboratoire de Mathématiques Appliquées LMA, CNRS UMR 7348, 86021 Poitiers, France
- Department of Genetic, University Hospital Center of Poitiers, 86000 Poitiers, France
| | - Clément Thomas
- Department of Imaging, University Hospital Center of Poitiers, 86000 Poitiers, France
- Labcom I3M, University of Poitiers, 86000 Poitiers, France
- DACTIM-MIS Team, Laboratoire de Mathématiques Appliquées LMA, CNRS UMR 7348, 86021 Poitiers, France
| | - Guillaume Herpe
- Department of Imaging, University Hospital Center of Poitiers, 86000 Poitiers, France
- Labcom I3M, University of Poitiers, 86000 Poitiers, France
- DACTIM-MIS Team, Laboratoire de Mathématiques Appliquées LMA, CNRS UMR 7348, 86021 Poitiers, France
| | - Alain Miranville
- Labcom I3M, University of Poitiers, 86000 Poitiers, France
- DACTIM-MIS Team, Laboratoire de Mathématiques Appliquées LMA, CNRS UMR 7348, 86021 Poitiers, France
| | | | - Luc Pellerin
- IRMETIST Laboratory, INSERM U1313, University of Poitiers and University Hospital Center of Poitiers, 86000 Poitiers, France
| | - Carole Guillevin
- Department of Imaging, University Hospital Center of Poitiers, 86000 Poitiers, France
- Labcom I3M, University of Poitiers, 86000 Poitiers, France
- DACTIM-MIS Team, Laboratoire de Mathématiques Appliquées LMA, CNRS UMR 7348, 86021 Poitiers, France
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Weber KA, Teplin ZM, Wager TD, Law CSW, Prabhakar NK, Ashar YK, Gilam G, Banerjee S, Delp SL, Glover GH, Hastie TJ, Mackey S. Confounds in neuroimaging: A clear case of sex as a confound in brain-based prediction. Front Neurol 2022; 13:960760. [PMID: 36601297 PMCID: PMC9806266 DOI: 10.3389/fneur.2022.960760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 11/25/2022] [Indexed: 12/23/2022] Open
Abstract
Muscle weakness is common in many neurological, neuromuscular, and musculoskeletal conditions. Muscle size only partially explains muscle strength as adaptions within the nervous system also contribute to strength. Brain-based biomarkers of neuromuscular function could provide diagnostic, prognostic, and predictive value in treating these disorders. Therefore, we sought to characterize and quantify the brain's contribution to strength by developing multimodal MRI pipelines to predict grip strength. However, the prediction of strength was not straightforward, and we present a case of sex being a clear confound in brain decoding analyses. While each MRI modality-structural MRI (i.e., gray matter morphometry), diffusion MRI (i.e., white matter fractional anisotropy), resting state functional MRI (i.e., functional connectivity), and task-evoked functional MRI (i.e., left or right hand motor task activation)-and a multimodal prediction pipeline demonstrated significant predictive power for strength (R 2 = 0.108-0.536, p ≤ 0.001), after correcting for sex, the predictive power was substantially reduced (R 2 = -0.038-0.075). Next, we flipped the analysis and demonstrated that each MRI modality and a multimodal prediction pipeline could significantly predict sex (accuracy = 68.0%-93.3%, AUC = 0.780-0.982, p < 0.001). However, correcting the brain features for strength reduced the accuracy for predicting sex (accuracy = 57.3%-69.3%, AUC = 0.615-0.780). Here we demonstrate the effects of sex-correlated confounds in brain-based predictive models across multiple brain MRI modalities for both regression and classification models. We discuss implications of confounds in predictive modeling and the development of brain-based MRI biomarkers, as well as possible strategies to overcome these barriers.
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Affiliation(s)
- Kenneth A. Weber
- Systems Neuroscience and Pain Lab, Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Palo Alto, CA, United States,*Correspondence: Kenneth A. Weber II
| | - Zachary M. Teplin
- Systems Neuroscience and Pain Lab, Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Palo Alto, CA, United States
| | - Tor D. Wager
- Department of Psychological and Brain Sciences, Dartmouth College, Hanover, NH, United States
| | - Christine S. W. Law
- Systems Neuroscience and Pain Lab, Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Palo Alto, CA, United States
| | - Nitin K. Prabhakar
- Division of Physical Medicine and Rehabilitation, Department of Orthopaedic Surgery, Stanford University School of Medicine, Palo Alto, CA, United States
| | - Yoni K. Ashar
- Department of Psychiatry, Weill Cornell Medicine, New York, NY, United States
| | - Gadi Gilam
- Systems Neuroscience and Pain Lab, Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Palo Alto, CA, United States,The Institute of Biomedical and Oral Research, Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | | | - Scott L. Delp
- Department of Bioengineering and Mechanical Engineering, Stanford University, Palo Alto, CA, United States
| | - Gary H. Glover
- Radiological Sciences Laboratory, Department of Radiology, Stanford University School of Medicine, Palo Alto, CA, United States
| | - Trevor J. Hastie
- Department of Statistics, Stanford University, Palo Alto, CA, United States
| | - Sean Mackey
- Systems Neuroscience and Pain Lab, Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Palo Alto, CA, United States
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Jing H, Yang F, Peng K, Qin D, He Y, Yang G, Zhang H. Multimodal MRI-Based Radiomic Nomogram for the Early Differentiation of Recurrence and Pseudoprogression of High-Grade Glioma. BIOMED RESEARCH INTERNATIONAL 2022; 2022:4667117. [PMID: 36246986 PMCID: PMC9553483 DOI: 10.1155/2022/4667117] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 09/15/2022] [Accepted: 09/17/2022] [Indexed: 11/18/2022]
Abstract
Objective To evaluate the diagnostic value of multimodal MRI radiomics based on T2-weighted fluid attenuated inversion recovery imaging (T2WI-FLAIR) combined with T1-weighted contrast enhanced imaging (T1WI-CE) in the early differentiation of high-grade glioma recurrence from pseudoprogression. Methods A total of one hundred eighteen patients with brain gliomas who were diagnosed from March 2014 to April 2020 were retrospectively analyzed. According to the clinical characteristics, the patients were randomly split into a training group (n = 83) and a test group (n = 35) at a 7 : 3 ratio. The region of interest (ROI) was delineated, and 2632 radiomic features were extracted. We used multiple logistic regression to establish a classification model, including the T1 model, T2 model, and T1 + T2 model, to differentiate recurrence from pseudoprogression. The diagnostic efficiency of the model was evaluated by calculating the area under the receiver operating characteristic curve (AUC) and accuracy (ACC) and by analyzing the calibration curve of the nomogram and decision curve. Results There were 75 cases of recurrence and 43 cases of pseudoprogression. The diagnostic efficacies of the multimodal MRI-based radiomic model were relatively high. The AUC values and ACC of the training group were 0.831 and 77.11%, respectively, and the AUC values and ACC of the test group were 0.829 and 88.57%, respectively. The calibration curve of the nomogram showed that the discrimination probability was consistent with the actual occurrence in the training group, and the discrimination probability was roughly the same as the actual occurrence in the test group. In the decision curve analysis, the T1 + T2 model showed greater overall net efficiency. Conclusion The multimodal MRI radiomic model has relatively high efficiency in the early differentiation of recurrence from pseudoprogression, and it could be helpful for clinicians in devising correct treatment plans so that patients can be treated in a timely and accurate manner.
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Affiliation(s)
- Hui Jing
- College of Medical Imaging, Shanxi Medical University, Taiyuan, Shanxi Province, China
- Department of Radiology, The Sixth Hospital, Shanxi Medical University, Taiyuan, Shanxi Province, China
| | - Fan Yang
- College of Medical Imaging, Shanxi Medical University, Taiyuan, Shanxi Province, China
| | - Kun Peng
- Department of Radiology, The Sixth Hospital, Shanxi Medical University, Taiyuan, Shanxi Province, China
| | - Danlei Qin
- College of Medical Imaging, Shanxi Medical University, Taiyuan, Shanxi Province, China
| | - Yexin He
- Department of Radiology, Shanxi Provincial People's Hospital, Affiliated People's Hospital of Shanxi Medical University, Taiyuan, China
| | - Guoqiang Yang
- Department of Radiology, First Clinical Medical College, Shanxi Medical University, Taiyuan, Shanxi Province, China
| | - Hui Zhang
- College of Medical Imaging, Shanxi Medical University, Taiyuan, Shanxi Province, China
- Department of Radiology, First Clinical Medical College, Shanxi Medical University, Taiyuan, Shanxi Province, China
- Shanxi Key Laboratory of Intelligent Imaging and Nanomedicine, Shanxi Medical University, Taiyuan, Shanxi Province, China
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