Deep Learning Segmentation of the Nucleus Basalis of Meynert on 3T MRI

References

1. 1.↵
   2. Liu AK,
   3. Chang RC,
   4. Pearce RK, et al

   . Nucleus basalis of Meynert revisited: anatomy, history and differential involvement in Alzheimer's and Parkinson's disease. Acta Neuropathol 2015;129:527–40 doi:10.1007/s00401-015-1392-5 pmid:25633602

   CrossRefPubMed
2. 2.↵
   2. Mesulam MM,
   3. Mufson EJ,
   4. Levey AI, et al

   . Cholinergic innervation of cortex by the basal forebrain: cytochemistry and cortical connections of the septal area, diagonal band nuclei, nucleus basalis (substantia innominata), and hypothalamus in the rhesus monkey. J Comp Neurol 1983;214:170–97 doi:10.1002/cne.902140206 pmid:6841683

   CrossRefPubMedWeb of Science
3. 3.↵
   2. Gonzalez HFJ,
   3. Narasimhan S,
   4. Johnson GW, et al

   . Role of the nucleus basalis as a key network node in temporal lobe epilepsy. Neurology 2021;96:e1334–46 doi:10.1212/WNL.0000000000011523 pmid:33441453

   Abstract/FREE Full Text
4. 4.↵
   2. Schulz J,
   3. Pagano G,
   4. Fernández Bonfante JA, et al

   . Nucleus basalis of Meynert degeneration precedes and predicts cognitive impairment in Parkinson's disease. Brain 2018;141:1501–16 doi:10.1093/brain/awy072 pmid:29701787

   CrossRefPubMed
5. 5.↵
   2. Whitehouse PJ,
   3. Price DL,
   4. Clark AW, et al

   . Alzheimer disease: evidence for selective loss of cholinergic neurons in the nucleus basalis. Ann Neurol 1981;10:122–26 doi:10.1002/ana.410100203 pmid:7283399

   CrossRefPubMedWeb of Science
6. 6.↵
   2. Schumacher J,
   3. Thomas AJ,
   4. Peraza LR, et al

   . Functional connectivity of the nucleus basalis of Meynert in Lewy body dementia and Alzheimer's disease. Int Psychogeriatr 2021;33:89–94 doi:10.1017/S1041610220003944 pmid:33413710

   CrossRefPubMed
7. 7.↵
   2. Oswal A,
   3. Gratwicke J,
   4. Akram H, et al

   . Cortical connectivity of the nucleus basalis of Meynert in Parkinson's disease and Lewy body dementias. Brain 2021;144:781–88 doi:10.1093/brain/awaa411 pmid:33521808

   CrossRefPubMed
8. 8.↵
   2. Chen YS,
   3. Shu K,
   4. Kang HC

   . Deep brain stimulation in Alzheimer's disease: targeting the nucleus basalis of Meynert. J Alzheimers Dis 2021;80:53–70 doi:10.3233/JAD-201141 pmid:33492288

   CrossRefPubMed
9. 9.↵
   2. Kuhn J,
   3. Hardenacke K,
   4. Lenartz D, et al

   . Deep brain stimulation of the nucleus basalis of Meynert in Alzheimer's dementia. Mol Psychiatry 2015;20:353–60 doi:10.1038/mp.2014.32 pmid:24798585

   CrossRefPubMed
10. 10.↵
    2. Wilson H,
    3. de Natale ER,
    4. Politis M

    . Nucleus basalis of Meynert degeneration predicts cognitive impairment in Parkinson's disease. Handb Clin Neurol 2021;179:189–205 doi:10.1016/B978-0-12-819975-6.00010-8 pmid:34225962

    CrossRefPubMed
11. 11.↵
    2. Zaborszky L,
    3. Hoemke L,
    4. Mohlberg H, et al

    . Stereotaxic probabilistic maps of the magnocellular cell groups in human basal forebrain. Neuroimage 2008;42:1127–41 doi:10.1016/j.neuroimage.2008.05.055 pmid:18585468

    CrossRefPubMedWeb of Science
12. 12.↵
    2. Eickhoff SB,
    3. Stephan KE,
    4. Mohlberg H, et al

    . A new SPM toolbox for combining probabilistic cytoarchitectonic maps and functional imaging data. Neuroimage 2005;25:1325–35 doi:10.1016/j.neuroimage.2004.12.034 pmid:15850749

    CrossRefPubMedWeb of Science
13. 13.↵
    2. Kim J,
    3. Duchin Y,
    4. Shamir RR, et al

    . Automatic localization of the subthalamic nucleus on patient-specific clinical MRI by incorporating 7 T MRI and machine learning: application in deep brain stimulation. Hum Brain Mapp 2019;40:679–98 doi:10.1002/hbm.24404 pmid:30379376

    CrossRefPubMed
14. 14.↵
    2. Kim J,
    3. Patriat R,
    4. Kaplan J, et al

    . Deep cerebellar nuclei segmentation via semi-supervised deep context-aware learning from 7T diffusion MRI. IEEE Access 2020;8:101550–68 doi:10.1109/access.2020.2998537 pmid:32656051

    CrossRefPubMed
15. 15.↵
    2. Greve DN,
    3. Billot B,
    4. Cordero D, et al

    . A deep learning toolbox for automatic segmentation of subcortical limbic structures from MRI images. Neuroimage 2021;244:118610 doi:10.1016/j.neuroimage.2021.118610 pmid:34571161

    CrossRefPubMed
16. 16.↵
    2. Billot B,
    3. Bocchetta M,
    4. Todd E, et al

    . Automated segmentation of the hypothalamus and associated subunits in brain MRI. Neuroimage 2020;223:117287 doi:10.1016/j.neuroimage.2020.117287 pmid:32853816

    CrossRefPubMed
17. 17.↵
    2. Wang Y,
    3. Zhan M,
    4. Roebroeck A, et al

    . Inconsistencies in atlas-based volumetric measures of the human nucleus basalis of Meynert: a need for high-resolution alternatives. Neuroimage 2022;259:119421 doi:10.1016/j.neuroimage.2022.119421

    CrossRefPubMed
18. 18.↵
    2. Niazi MK,
    3. Parwani AV,
    4. Gurcan MN

    . Digital pathology and artificial intelligence. Lancet Oncol 2019;20:e253–61 doi:10.1016/S1470-2045(19)30154-8 pmid:31044723

    CrossRefPubMed
19. 19.↵
    2. Isaacs BR,
    3. Mulder MJ,
    4. Groot JM, et al

    . 3 versus 7 Tesla magnetic resonance imaging for parcellations of subcortical brain structures in clinical settings. PLoS One 2020;15:e0236208 doi:10.1371/journal.pone.0236208 pmid:33232325

    CrossRefPubMed
20. 20.↵
    2. Liu Y,
    3. D'Haese PF,
    4. Newton AT, et al

    . Generation of human thalamus atlases from 7T data and application to intrathalamic nuclei segmentation in clinical 3T T1-weighted images. Magn Reson Imaging 2020;65:114–28 doi:10.1016/j.mri.2019.09.004 pmid:31629074

    CrossRefPubMed
21. 21.↵
    2. Ramadass K,
    3. Rheault F,
    4. Cai LY, et al

    . Ultra-high-resolution mapping of cortical layers 3T-guided 7T MRI. Proc SPIE Int Soc Opt Eng 2022;12032:120321G doi:10.1117/12.2611857 pmid:36303575

    CrossRefPubMed
22. 22.↵
    2. Jethwa K,
    3. Aphiwatthanasumet K,
    4. Mougin O, et al

    . Phase enhanced PSIR T1-weighted imaging improves contrast resolution of the nucleus basalis of Meynert at 7T: a preliminary study. Magn Reson Imaging 2019;61:296–99 doi:10.1016/j.mri.2019.06.004 pmid:31202788

    CrossRefPubMed
23. 23.↵
    2. D'Haese PF,
    3. Pallavaram S,
    4. Li R, et al

    . CranialVault and its CRAVE tools: a clinical computer assistance system for deep brain stimulation (DBS) therapy. Med Image Anal 2012;16:744–53 doi:10.1016/j.media.2010.07.009 pmid:20732828

    CrossRefPubMed
24. 24.↵
    2. Brett M,
    3. Markiewicz CJ,
    4. Hanke M, et al

    . nipy/nibabel: 4.0.0rc0. 2022/6/2022 doi:10.5281/ZENODO.6617127

    CrossRef
25. 25.↵
    2. Iglesias JE,
    3. Liu CY,
    4. Thompson PM, et al

    . Robust brain extraction across datasets and comparison with publicly available methods. IEEE Trans Med Imaging 2011;30:1617–34 doi:10.1109/TMI.2011.2138152 pmid:21880566

    CrossRefPubMedWeb of Science
26. 26.↵
    2. Pérez-García F,
    3. Sparks R,
    4. Ourselin S

    . TorchIO: a Python library for efficient loading, preprocessing, augmentation and patch-based sampling of medical images in deep learning. Comput Methods Programs Biomed 2021;208:106236 doi:10.1016/j.cmpb.2021.106236 pmid:34311413

    CrossRefPubMed
27. 27.↵
    1. Navab N,
    2. Hornegger J,
    3. Wells WM, et al.

    2. Ronneberger O,
    3. Fischer P,
    4. Brox T

    . U-net: Convolutional networks for biomedical image segmentation. In: Navab N, Hornegger J, Wells WM, et al., eds. Medical Image Computing and Computer-Assisted Intervention–MICCAI 2015. Springer; 2015: 234–41
28. 28.↵
    2. Taha AA,
    3. Hanbury A

    . Metrics for evaluating 3D medical image segmentation: analysis, selection, and tool. BMC Med Imaging 2015;15:29 doi:10.1186/s12880-015-0068-x pmid:26263899

    CrossRefPubMed
29. 29.↵
    2. Bergstra J,
    3. Yamins D,
    4. Cox D

    . Making a science of model search: hyperparameter optimization in hundreds of dimensions for vision architectures. Proceedings of the 30th International Conference on Machine Learning, 2013. https://proceedings.mlr.press/v28/bergstra13.html. Accessed November 11, 2022
30. 30.↵
    2. Dice LR

    . Measures of the amount of ecologic association between species. Ecology 1945;26:297–302 doi:10.2307/1932409

    CrossRefWeb of Science
31. 31.↵
    2. Trutti AC,
    3. Fontanesi L,
    4. Mulder MJ, et al

    . A probabilistic atlas of the human ventral tegmental area (VTA) based on 7 Tesla MRI data. Brain Struct Funct 2021;226:1155–67 doi:10.1007/s00429-021-02231-w pmid:33580320

    CrossRefPubMed
32. 32.↵
    2. Cantero JL,
    3. Zaborszky L,
    4. Atienza M

    . Volume loss of the nucleus basalis of Meynert is associated with atrophy of innervated regions in mild cognitive impairment. Cereb Cortex 2017;27:3881–89 doi:10.1093/cercor/bhw195 pmid:27371762

    CrossRefPubMed
33. 33.↵
    2. Grothe M,
    3. Heinsen H,
    4. Teipel SJ

    . Atrophy of the cholinergic basal forebrain over the adult age range and in early stages of Alzheimer's disease. Biol Psychiatry 2012;71:805–13 doi:10.1016/j.biopsych.2011.06.019 pmid:21816388

    CrossRefPubMedWeb of Science
34. 34.↵
    2. Kilimann I,
    3. Grothe M,
    4. Heinsen H, et al

    . Subregional basal forebrain atrophy in Alzheimer's disease: a multicenter study. J Alzheimers Dis 2014;40:687–700 doi:10.3233/JAD-132345 pmid:24503619

    Abstract/FREE Full Text
35. 35.↵
    2. Kim HJ,
    3. Lee JE,
    4. Shin SJ, et al

    . Analysis of the substantia innominata volume in patients with Parkinson's disease with dementia, dementia with Lewy bodies, and Alzheimer's disease. J Mov Disord 2011;4:68–72 doi:10.14802/jmd.11014 pmid:24868398

    CrossRefPubMed
36. 36.↵
    2. Lammers F,
    3. Borchers F,
    4. Feinkohl I, et al

    ; BioCog consortium. Basal forebrain cholinergic system volume is associated with general cognitive ability in the elderly. Neuropsychologia 2018;119:145–56 doi:10.1016/j.neuropsychologia.2018.08.005 pmid:30096414

    CrossRefPubMed
37. 37.↵
    2. Ray NJ,
    3. Bradburn S,
    4. Murgatroyd C, et al

    . In vivo cholinergic basal forebrain atrophy predicts cognitive decline in de novo Parkinson's disease. Brain 2018;141:165–76 doi:10.1093/brain/awx310 pmid:29228203

    CrossRefPubMed
38. 38.↵
    2. Rong S,
    3. Li Y,
    4. Li B, et al

    . Meynert nucleus-related cortical thinning in Parkinson's disease with mild cognitive impairment. Quant Imaging Med Surg 2021;11:1554–66 doi:10.21037/qims-20-444 pmid:33816191

    CrossRefPubMed
39. 39.↵
    2. Scheef L,
    3. Grothe MJ,
    4. Koppara A, et al

    . Subregional volume reduction of the cholinergic forebrain in subjective cognitive decline (SCD). Neuroimage Clin 2019;21:101612 doi:10.1016/j.nicl.2018.101612 pmid:30555006

    CrossRefPubMed
40. 40.↵
    2. Wolf D,
    3. Grothe M,
    4. Fischer FU, et al

    . Association of basal forebrain volumes and cognition in normal aging. Neuropsychologia 2014;53:54–63 doi:10.1016/j.neuropsychologia.2013.11.002 pmid:24269297

    CrossRefPubMedWeb of Science