Mitigating the Impact of MR Sequence Parameters: Increasing the Robustness of DL-Based Cortical Thickness Estimates.
Overview
- Support Center for Advanced Neuroimaging (SCAN), University Institute of Diagnostic and Interventional Neuroradiology University of Bern, Inselspital, Bern University Hospital Bern Switzerland
- Balgrist University Hospital Zurich Switzerland
- Department of Neurology, Inselspital Bern University Hospital and University of Bern Bern Switzerland
- Translational Imaging Center (TIC) Swiss Institute for Translational and Entrepreneurial Medicine, Sitem‐Insel Bern Switzerland
- European Campus Rottal‐Inn Technische Hochschule Deggendorf Pfarrkirchen Germany
- High‐Field MR Center Max Planck Institute for Biological Cybernetics Tübingen Germany
Abstract
Cortical thickness measurements from MRI are increasingly used as biomarkers for neurodegenerative disease progression. However, variations in MRI acquisition parameters, such as inversion time (TI) and repetition time (TR), which are common in clinical settings, can compromise the reliability and sensitivity of these measurements. We fine‐tuned a deep‐learning‐based segmentation tool (DL+DiReCT) to reduce its dependence to image contrast variations by training it on simulated MPRAGE images derived from quantitative relaxation maps. Fine‐tuning markedly reduced contrast sensitivity, with the Pearson correlation coefficient decreasing from −0.644 to 0.094. Evaluation on a synthetic atrophy dataset demonstrated that our model accurately replicated atrophy trends with minimal underestimation, outperforming FreeSurfer and SynthSeg. When applied to a dataset of relapsing–remitting multiple sclerosis (RRMS) patients, the fine‐tuned model showed a substantial reduction in contrast sensitivity and maintained stable performance after controlling for covariates such as age, sex, field strength, and Expanded Disability Status Scale (EDSS) score. Overall, the proposed approach achieves robust contrast invariance without sacrificing sensitivity to cortical atrophy, offering a practical improvement for longitudinal and multi‐center clinical studies.
Reproduced under the paper's license (CC BY), from the paper cited above.
Code
The paper links to its data, not to its authors' code: see the Data section.
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Data
Datasets cited
- openneuro:ds004560, at OpenNeuro; found in the references
Data Availability Statement
Training dataset: this training dataset is publicly available (Clark and Maguire 2023). Contrast sensitivity: this evaluation dataset is publicly available (Rebsamen, Romascano, et al. 2023). Atrophy sensitivity: this evaluation dataset is publicly available (Rusak et al. 2021). MS evaluation: this evaluation dataset is not publicly available.
Reproduced under the paper's license (CC BY), from the paper cited above.
Versions
The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.
Version 1, 27 September 2026: the first record
Recorded: type, language, journal, volume, issue, pages, dates, 11 authors, 7 keywords, 13 MeSH terms, 1 funder, 43 references.
Cite
This paper
Blattner, T., Romascano, D., McKinley, R., Rebsamen, M., Salmen, A., Pistor, M., Hoepner, R., Wiest, R., Radojewski, P., Rummel, C., & Capiglioni, M. (2026). Mitigating the Impact of MR Sequence Parameters: Increasing the Robustness of DL-Based Cortical Thickness Estimates. Human brain mapping, 47(8), e70560. https://
BibTeX
@article{blattner2026mit
author = {Blattner, Timo and Romascano, David and McKinley, Richard and Rebsamen, Michael and Salmen, Anke and Pistor, Maximilian and Hoepner, Robert and Wiest, Roland and Radojewski, Piotr and Rummel, Christian and Capiglioni, Milena},
title = {{Mitigating the Impact of MR Sequence Parameters: Increasing the Robustness of DL-Based Cortical Thickness Estimates}},
journal = {Human brain mapping},
year = {2026},
month = jun,
volume = {47},
number = {8},
pages = {e70560},
publisher = {Wiley},
issn = {1065-9471},
doi = {10.1002/
url = {https://
pmid = {42252567},
pmcid = {PMC13243191}
}
RIS
TY - JOUR
AU - Blattner, Timo
AU - Romascano, David
AU - McKinley, Richard
AU - Rebsamen, Michael
AU - Salmen, Anke
AU - Pistor, Maximilian
AU - Hoepner, Robert
AU - Wiest, Roland
AU - Radojewski, Piotr
AU - Rummel, Christian
AU - Capiglioni, Milena
TI - Mitigating the Impact of MR Sequence Parameters: Increasing the Robustness of DL-Based Cortical Thickness Estimates
T2 - Human brain mapping
J2 - Hum Brain Mapp
PY - 2026
DA - 2026/
VL - 47
IS - 8
SP - e70560
SN - 1065-9471
PB - Wiley
DO - 10.1002/
UR - https://
LA - en
ER -
CSL-JSON
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