BigBrain-MR: a new digital phantom with anatomically-realistic magnetic resonance properties at 100-µm resolution for magnetic resonance methods development
The benefits, opportunities and growing availability of ultra-high field magnetic resonance imaging (MRI) for humans have prompted an expansion in research and development efforts towards increasingly more advanced high-resolution imaging techniques. To maximize their effectiveness, these efforts ne...
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2023-06-01
|
| Series: | NeuroImage |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S1053811923002203 |
| _version_ | 1797837193276817408 |
|---|---|
| author | Cristina Sainz Martinez Meritxell Bach Cuadra João Jorge |
| author_facet | Cristina Sainz Martinez Meritxell Bach Cuadra João Jorge |
| author_sort | Cristina Sainz Martinez |
| collection | DOAJ |
| description | The benefits, opportunities and growing availability of ultra-high field magnetic resonance imaging (MRI) for humans have prompted an expansion in research and development efforts towards increasingly more advanced high-resolution imaging techniques. To maximize their effectiveness, these efforts need to be supported by powerful computational simulation platforms that can adequately reproduce the biophysical characteristics of MRI, with high spatial resolution. In this work, we have sought to address this need by developing a novel digital phantom with realistic anatomical detail up to 100-µm resolution, including multiple MRI properties that affect image generation. This phantom, termed BigBrain-MR, was generated from the publicly available BigBrain histological dataset and lower-resolution in-vivo 7T-MRI data, using a newly-developed image processing framework that allows mapping the general properties of the latter into the fine anatomical scale of the former. Overall, the mapping framework was found to be effective and robust, yielding a diverse range of realistic “in-vivo-like” MRI contrasts and maps at 100-µm resolution. BigBrain-MR was then tested in three imaging applications (motion effects and interpolation, super-resolution imaging, and parallel imaging reconstruction) to investigate its properties, value and validity as a simulation platform. The results consistently showed that BigBrain-MR can closely approximate the behavior of real in-vivo data, more realistically and with more extensive features than a more classic option such as the Shepp-Logan phantom. Its flexibility in simulating different contrast mechanisms and artifacts may also prove valuable for educational applications. BigBrain-MR is therefore deemed a favorable choice to support methodological development and demonstration in brain MRI, and has been made freely available to the community. |
| first_indexed | 2024-04-09T15:20:52Z |
| format | Article |
| id | doaj.art-cba5be79acb847c2a568c62981cb3f38 |
| institution | Directory Open Access Journal |
| issn | 1095-9572 |
| language | English |
| last_indexed | 2024-04-09T15:20:52Z |
| publishDate | 2023-06-01 |
| publisher | Elsevier |
| record_format | Article |
| series | NeuroImage |
| spelling | doaj.art-cba5be79acb847c2a568c62981cb3f382023-04-29T14:47:07ZengElsevierNeuroImage1095-95722023-06-01273120074BigBrain-MR: a new digital phantom with anatomically-realistic magnetic resonance properties at 100-µm resolution for magnetic resonance methods developmentCristina Sainz Martinez0Meritxell Bach Cuadra1João Jorge2CSEM - Swiss Center for Electronics and Microtechnology, Switzerland; CIBM Center for Biomedical Imaging, SwitzerlandCIBM Center for Biomedical Imaging, Switzerland; Department of Radiology, Lausanne University Hospital and University of Lausanne, SwitzerlandCSEM - Swiss Center for Electronics and Microtechnology, Switzerland; Corresponding author at: Freiburgstrasse 2, 3008 Bern, SwitzerlandThe benefits, opportunities and growing availability of ultra-high field magnetic resonance imaging (MRI) for humans have prompted an expansion in research and development efforts towards increasingly more advanced high-resolution imaging techniques. To maximize their effectiveness, these efforts need to be supported by powerful computational simulation platforms that can adequately reproduce the biophysical characteristics of MRI, with high spatial resolution. In this work, we have sought to address this need by developing a novel digital phantom with realistic anatomical detail up to 100-µm resolution, including multiple MRI properties that affect image generation. This phantom, termed BigBrain-MR, was generated from the publicly available BigBrain histological dataset and lower-resolution in-vivo 7T-MRI data, using a newly-developed image processing framework that allows mapping the general properties of the latter into the fine anatomical scale of the former. Overall, the mapping framework was found to be effective and robust, yielding a diverse range of realistic “in-vivo-like” MRI contrasts and maps at 100-µm resolution. BigBrain-MR was then tested in three imaging applications (motion effects and interpolation, super-resolution imaging, and parallel imaging reconstruction) to investigate its properties, value and validity as a simulation platform. The results consistently showed that BigBrain-MR can closely approximate the behavior of real in-vivo data, more realistically and with more extensive features than a more classic option such as the Shepp-Logan phantom. Its flexibility in simulating different contrast mechanisms and artifacts may also prove valuable for educational applications. BigBrain-MR is therefore deemed a favorable choice to support methodological development and demonstration in brain MRI, and has been made freely available to the community.http://www.sciencedirect.com/science/article/pii/S1053811923002203Magnetic resonance imagingUltra-high fieldBrainPhantomBigBrain |
| spellingShingle | Cristina Sainz Martinez Meritxell Bach Cuadra João Jorge BigBrain-MR: a new digital phantom with anatomically-realistic magnetic resonance properties at 100-µm resolution for magnetic resonance methods development NeuroImage Magnetic resonance imaging Ultra-high field Brain Phantom BigBrain |
| title | BigBrain-MR: a new digital phantom with anatomically-realistic magnetic resonance properties at 100-µm resolution for magnetic resonance methods development |
| title_full | BigBrain-MR: a new digital phantom with anatomically-realistic magnetic resonance properties at 100-µm resolution for magnetic resonance methods development |
| title_fullStr | BigBrain-MR: a new digital phantom with anatomically-realistic magnetic resonance properties at 100-µm resolution for magnetic resonance methods development |
| title_full_unstemmed | BigBrain-MR: a new digital phantom with anatomically-realistic magnetic resonance properties at 100-µm resolution for magnetic resonance methods development |
| title_short | BigBrain-MR: a new digital phantom with anatomically-realistic magnetic resonance properties at 100-µm resolution for magnetic resonance methods development |
| title_sort | bigbrain mr a new digital phantom with anatomically realistic magnetic resonance properties at 100 µm resolution for magnetic resonance methods development |
| topic | Magnetic resonance imaging Ultra-high field Brain Phantom BigBrain |
| url | http://www.sciencedirect.com/science/article/pii/S1053811923002203 |
| work_keys_str_mv | AT cristinasainzmartinez bigbrainmranewdigitalphantomwithanatomicallyrealisticmagneticresonancepropertiesat100μmresolutionformagneticresonancemethodsdevelopment AT meritxellbachcuadra bigbrainmranewdigitalphantomwithanatomicallyrealisticmagneticresonancepropertiesat100μmresolutionformagneticresonancemethodsdevelopment AT joaojorge bigbrainmranewdigitalphantomwithanatomicallyrealisticmagneticresonancepropertiesat100μmresolutionformagneticresonancemethodsdevelopment |