Comparative analysis of freesurfer and brainsuite in thickness, surface area, and volume measurements for morphometric group comparisons

Akhil, M., Aishwarya, R., Lal, V., & Mahesh, S. (2016). Comparison and evaluation of segmentation techniques for brain MRI using gold standard. Indian Journal of Science and Technology, 9(46), 1–5. https://doi.org/10.17485/ijst/2016/v9i46/106495

Article  CAS  Google Scholar 

Ambarki, K., Wåhlin, A., Birgander, R., Eklund, A., & Malm, J. (2011). MR imaging of brain volumes: Evaluation of a fully automatic software. American Journal of Neuroradiology, 32(2), 408–412. https://doi.org/10.3174/ajnr.A2275

Article  CAS  PubMed  Google Scholar 

Amunts, K., Jäncke, L., Mohlberg, H., Steinmetz, H., & Zilles, K. (2000). Interhemispheric asymmetry of the human motor cortex related to handedness and gender. Neuropsychologia, 38(3), 304–312. https://doi.org/10.1016/S0028-3932(99)00075-5

Article  CAS  PubMed  Google Scholar 

Barnes, J., Ridgway, G. R., Bartlett, J., Henley, S. M., Lehmann, M., Hobbs, N., & Fox, N. C. (2010). Head size, age and gender adjustment in MRI studies: A necessary nuisance? NeuroImage, 53(4), 1244–1255. https://doi.org/10.1016/j.neuroimage.2010.06.025

Article  PubMed  Google Scholar 

Chaves, H., Dorr, F., Costa, M. E., Serra, M. M., Slezak, D. F., Farez, M. F., & Cejas, C. (2021). Brain volumes quantification from MRI in healthy controls: Assessing correlation, agreement and robustness of a convolutional neural network-based software against FreeSurfer, CAT12 and FSL. Journal of Neuroradiology, 48(3), 147–156. https://doi.org/10.1016/j.neurad.2020.10.001

Article  PubMed  Google Scholar 

DeCasien, A. R., Guma, E., Liu, S., & Raznahan, A. (2022). Sex differences in the human brain: A roadmap for more careful analysis and interpretation of a biological reality. Biology of Sex Differences, 13(1), Article 43. https://doi.org/10.1186/s13293-022-00448-w

Article  PubMed  PubMed Central  Google Scholar 

Desikan, R. S., Ségonne, F., Fischl, B., Quinn, B. T., Dickerson, B. C., Blacker, D., Buckner, R. L., Dale, A. M., Maguire, R. P., Albert, M. S., Killiany, R. J., & Hyman, B. T. (2006). An automated labeling system for subdividing the human cerebral cortex on MRI scans into gyral based regions of interest. NeuroImage, 31(3), 968–980. https://doi.org/10.1016/j.neuroimage.2006.01.021

Article  PubMed  Google Scholar 

Fischl, B. (2012). FreeSurfer. NeuroImage, 62(2), 774–781. https://doi.org/10.1016/j.neuroimage.2012.01.021

Article  PubMed  PubMed Central  Google Scholar 

Fischl, B., & Dale, A. M. (2000). Measuring the thickness of the human cerebral cortex from magnetic resonance images. Proceedings of the National Academy of Sciences, 97(20), 11050–11055. https://doi.org/10.1073/pnas.200033797

Article  CAS  Google Scholar 

Fjell, A. M., Walhovd, K. B., Reinvang, I., Lundervold, A., Salat, D., Quinn, B. T., & Dale, A. M. (2006). Selective increase of cortical thickness in high-performing elderly—structural indices of optimal cognitive aging. NeuroImage, 29(3), 984–994. https://doi.org/10.1016/j.neuroimage.2005.08.007

Article  PubMed  Google Scholar 

Geng, D.-y, Li, Y.-X., & Zee, C.-S. (2006). Magnetic resonance imaging-based volumetric analysis of basal ganglia nuclei and substantia nigra in patients with Parkinson’s disease. Neurosurgery, 58(2), 256–262.

Article  PubMed  Google Scholar 

González-Villà, S., Oliver, A., Valverde, S., Wang, L., Zwiggelaar, R., & Lladó, X. (2016). A review on brain structures segmentation in magnetic resonance imaging. Artificial Intelligence in Medicine, 73, 45–69. https://doi.org/10.1016/j.artmed.2016.09.001

Article  PubMed  Google Scholar 

Han, X., Jovicich, J., Salat, D., van der Kouwe, A., Quinn, B., Czanner, S., & Killiany, R. (2006). Reliability of MRI-derived measurements of human cerebral cortical thickness: The effects of field strength, scanner upgrade and manufacturer. NeuroImage, 32(1), 180–194. https://doi.org/10.1016/j.neuroimage.2006.02.051

Article  PubMed  Google Scholar 

Iglesias, J. E., Insausti, R., Lerma-Usabiaga, G., Bocchetta, M., Van Leemput, K., Greve, D. N., & Paz-Alonso, P. M. (2018). A probabilistic atlas of the human thalamic nuclei combining ex vivo MRI and histology. NeuroImage, 183, 314–326.

Article  PubMed  PubMed Central  Google Scholar 

Ingalhalikar, M., Smith, A., Parker, D., Satterthwaite, T. D., Elliott, M. A., Ruparel, K., Hakonarson, Hakon, Gur, Raquel E.., Gur, Ruben C.., & Verma, R. (2014). Sex differences in the structural connectome of the human brain. Proceedings of the National Academy of Sciences, 111(2), 823–828. https://doi.org/10.1073/pnas.1316909110

Article  CAS  Google Scholar 

Joshi, A. A., Bhushan, C., Salloum, R., Wisnowski, J., Shattuck, D. W., & Leahy, R. M. (2018). Using the anisotropic Laplace equation to compute cortical thickness. Medical Image Computing and Computer-Assisted Intervention, 11072, 549–556. https://doi.org/10.1007/978-3-030-00931-1_63

Article  PubMed  PubMed Central  Google Scholar 

Kaczkurkin, A. N., Raznahan, A., & Satterthwaite, T. D. (2019). Sex differences in the developing brain: Insights from multimodal neuroimaging. Neuropsychopharmacology, 44(1), 71–85. https://doi.org/10.1038/s41386-018-0111-z

Article  PubMed  Google Scholar 

Kazemi, K., & Noorizadeh, N. (2014). Quantitative comparison of SPM, FSL, and brainsuite for brain MR image segmentation. Journal of Biomedical Physics and Engineering, 4(1).

Keller, S. S., Gerdes, J. S., Mohammadi, S., Kellinghaus, C., Kugel, H., Deppe, K., & Deppe, M. (2012). Volume estimation of the thalamus using freesurfer and stereology: Consistency between methods. Neuroinformatics, 10, 341–350. https://doi.org/10.1007/s12021-012-9147-0

Article  PubMed  PubMed Central  Google Scholar 

Klauschen, F., Goldman, A., Barra, V., Meyer-Lindenberg, A., & Lundervold, A. (2009). Evaluation of automated brain MR image segmentation and volumetry methods (pp. 1065–9471).

Lerch, J. P., & Evans, A. C. (2005). Cortical thickness analysis examined through power analysis and a population simulation. NeuroImage, 24(1), 163–173. https://doi.org/10.1016/j.neuroimage.2004.07.045

Article  PubMed  Google Scholar 

Litjens, G., Kooi, T., Bejnordi, B. E., Setio, A. A. A., Ciompi, F., Ghafoorian, M., & Sánchez, C. I. (2017). A survey on deep learning in medical image analysis. Medical Image Analysis, 42, 60–88. https://doi.org/10.1016/j.media.2017.07.005

Article  PubMed  Google Scholar 

Manjunath, K. (2002a). Estimation of cranial volume-an overview of methodologies. Journal of Anatomical Society of India, 51(1), 85–91.

Google Scholar 

Manjunath, K. (2002b). Estimation of cranial volume in dissecting room cadavers. Journal of Anatomical Society of India, 51(2), 168–172.

Google Scholar 

Mikhael, S. S., & Pernet, C. (2019). A controlled comparison of thickness, volume and surface areas from multiple cortical parcellation packages. BMC Bioinformatics, 20(1), 1–12. https://doi.org/10.1186/s12859-019-2609-8

Article  Google Scholar 

Mikhael, S., Hoogendoorn, C., Valdes-Hernandez, M., & Pernet, C. (2018). A critical analysis of neuroanatomical software protocols reveals clinically relevant differences in parcellation schemes. NeuroImage, 170, 348–364. https://doi.org/10.1016/j.neuroimage.2017.02.082

Article  PubMed  Google Scholar 

Narr, K. L., Thompson, P. M., Sharma, T., Moussai, J., Zoumalan, C., Rayman, J., & Toga, A. W. (2001). Three-dimensional mapping of gyral shape and cortical surface asymmetries in schizophrenia: Gender effects. American Journal of Psychiatry, 158(2), 244–255. https://doi.org/10.1176/appi.ajp.158.2.244

Article  CAS  PubMed  PubMed Central  Google Scholar 

Palumbo, L., Bosco, P., Fantacci, M., Ferrari, E., Oliva, P., Spera, G., & Retico, A. (2019). Evaluation of the intra-and inter-method agreement of brain MRI segmentation software packages: A comparison between SPM12 and freesurfer v6. 0. Physica Medica, 64, 261–272. https://doi.org/10.1016/j.ejmp.2019.07.016

Article  CAS  PubMed  Google Scholar 

Pantazis, D., Joshi, A., Jiang, J., Shattuck, D. W., Bernstein, L. E., Damasio, H., & Leahy, R. M. (2010). Comparison of landmark-based and automatic methods for cortical surface registration. NeuroImage, 49(3), 2479–2493. https://doi.org/10.1016/j.neuroimage.2009.09.027

Article  PubMed  Google Scholar 

Rosas, H. D., Salat, D. H., Lee, S. Y., Zaleta, A. K., Pappu, V., Fischl, B., & Hersch, S. M. (2008). Cerebral cortex and the clinical expression of Huntington’s disease: Complexity and heterogeneity. Brain, 131(4), 1057–1068. https://doi.org/10.1093/brain/awn025

Article  PubMed  PubMed Central  Google Scholar 

Ruigrok, A. N., Salimi-Khorshidi, G., Lai, M.-C., Baron-Cohen, S., Lombardo, M. V., Tait, R. J., & Suckling, J. (2014). A meta-analysis of sex differences in human brain structure. Neuroscience and Biobehavioral Reviews, 39, 34–50. https://doi.org/10.1016/j.neubiorev.2013.12.004

Article  PubMed  Google Scholar 

Seiger, R., Ganger, S., Kranz, G. S., Hahn, A., & Lanzenberger, R. (2018). Cortical thickness estimations of freesurfer and the CAT12 toolbox in patients with Alzheimer’s disease and healthy controls. Journal of Neuroimaging, 28(5), 515–523. https://doi.org/10.1111/jon.1252

Comments (0)

No login
gif