BRAHMA: Population specific T1, T2, and FLAIR weighted brain templates and their impact in structural and functional imaging studies

Pai, Praful P.; Mandal, Pravat K.; Punjabi, Khushboo; Shukla, Deepika; Goel, Anshika; Joon, Shallu; Roy, Saurav; Sandal, Kanika; Mishra, Ritwick; Lahoti, Ritu

doi:10.1016/j.mri.2019.12.009

Cited by 16 publications

(12 citation statements)

References 67 publications

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“…These should form useful reference templates and region maps for brain imaging studies involving predominantly Indian populations. Both the creation of age‐specific templates and the inclusion of associated atlases make the present study distinct from previous Indian population brain template projects (Bhalerao et al, 2018; Pai et al, 2020; Rao et al, 2017; Sivaswamy et al, 2019); additionally, we have generated both “population mean” and high‐contrast “typical” templates for each age band. The IBT volumes and corresponding atlases are publicly available for download, in standard NIFTI format, and freely usable by the wider neuroimaging community.…”

Section: Discussionmentioning

confidence: 95%

“…Finally, we investigated the practical difference when using IBT versus MNI as a template space for fMRI processing, using the valida- previous Indian population brain template projects (Bhalerao et al, 2018;Pai et al, 2020;Rao et al, 2017;Sivaswamy et al, 2019); additionally, we have generated both "population mean" and highcontrast "typical" templates for each age band. The IBT volumes and corresponding atlases are publicly available for download, in standard NIFTI format, and freely usable by the wider neuroimaging community.…”

Section: Resultsmentioning

confidence: 99%

“…The benefit of utilizing a population‐representative template in the Indian context has also been recognized, with the additional need for age‐specific templates due to the increasingly wide range of ages enrolled in studies. Recent attempts at developing brain templates for Indian population have tended to focus on the young adult age group (21–30 years) with relatively small (Rao et al, 2017) to modest sample sizes (Bhalerao et al, 2018; Pai et al, 2020; Sivaswamy et al, 2019), and have utilized data from a single site/scanner. Additionally, to date, whole‐brain annotated reference atlases based on segmentation have not accompanied the generated templates.…”

Section: Introductionmentioning

confidence: 99%

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A series of five population‐specific Indian brain templates and atlases spanning ages 6–60 years

Holla

Taylor²,

Glen³

et al. 2020

Human Brain Mapping

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Anatomical brain templates are commonly used as references in neurological MRI studies, for bringing data into a common space for group-level statistics and coordinate reporting. Given the inherent variability in brain morphology across age and geography, it is important to have templates that are as representative as possible for both age and population. A representative-template increases the accuracy of alignment, decreases distortions as well as potential biases in final coordinate reports. In this study, we developed and validated a new set of T1w Indian brain templates (IBT) from a large number of brain scans (total n = 466) acquired across different locations and multiple 3T MRI scanners in India. A new tool in AFNI, make_template_dask.py, was created to efficiently make five age-specific IBTs (ages 6-60 years) as well as maximum probability map (MPM) atlases for each template; for each age-group's template-atlas pair, there is both a "population-average" and a "typical" version. Validation experiments on an independent Indian structural and functional-MRI Bharath Holla and Paul A. Taylor are the equally contributing authors.

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Section: Discussionmentioning

confidence: 95%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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A series of five population‐specific Indian brain templates and atlases spanning ages 6–60 years

Holla

Taylor²,

Glen³

et al. 2020

Human Brain Mapping

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“…Currently available tools employ non-linear deformation fields for normalization of individual images as part of an unbiased iterative averaging process that produce improved detail and contrast (Avants et al, 2010). Furthermore, the Watanabe and Saikali brain templates are T1-weighted, whereas diffusion-weighted imaging (DWI) provides important additional information about white matter organization, and T2-weighted MRI can provide enhanced visualization of several important deep brain structures owing to their iron content (red nucleus, substantia nigra pars reticulata, globus pallidus) (Lalys et al, 2010;Telford and Vattoth, 2014;Pai et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

In vivo Population Averaged Stereotaxic T2w MRI Brain Template for the Adult Yucatan Micropig

et al. 2020

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“…The benefit of utilizing a population-representative template in the Indian context has also been recognized, with the additional need for age-specific templates due to the increasingly wide range of ages enrolled in studies. Recent attempts at developing brain templates for Indian population have tended to focus on the young adult age group (21-30 years) with relatively small [Rao et al, 2017] to modest sample sizes [Sivaswamy et al, 2019, Bhalerao et al, 2018, Pai et al, 2020], and have utilized data from a single site/scanner. Additionally, to date, whole-brain annotated reference atlases based on segmentation have not accompanied the generated templates.…”

Section: Introductionmentioning

confidence: 99%

A series of five population-specific Indian brain templates and atlases spanning ages 6 to 60 years

Holla

Taylor

Glen

et al. 2020

Preprint

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24Anatomical brain templates are commonly used as references in neurological MRI studies, for 25 bringing data into a common space for group level statistics and coordinate reporting. Having 26 a group representative template increases the accuracy of alignment, improves statistics and 27 decreases distortions (as well as potential biases) in final coordinate reports. Given the inherent 28 variability in brain morphology across age and geography, it is important to have templates 29 that are as representative as possible for both age and population. In this study, we developed 30 and validated a new set of T1w Indian brain templates (IBT) from a large number of subjects 31 (total n=466) across different Indian states and acquired at multiple 3T MRI sites. A new 32 tool in AFNI, make_template_dask.py, which uses the Dask python parallelization library, was 33 created to efficiently make a template from a group of subjects. A total of five age-specific 34 1 categories of IBTs [ages 6-11 yrs (C1), 12-18 yrs (C2), 19-25 yrs (C3), 26-40 yrs (C4), and 35 41-60 yrs (C5)], as well as maximum probability map (MPM) atlases for each template were 36 generated; for each age group's template-atlas pair, there is both a "population average" and a 37 "typical" version. Validation experiments on an independent Indian structural and functional 38 MRI dataset show the appropriateness of IBTs for spatial normalization of Indian brains. The 39 results indicate significant structural differences when comparing the IBTs and MNI template, 40 with these differences being maximal along the Anterior-Posterior and Inferior-Superior axes, 41 but minimal Left-Right. For each age group, the MPM brain atlases provide reasonably good 42 representation of the native-space volumes in the IBT space, except in a few regions with high 43 inter-subject variability as indicated by high mean deformation value. These findings provide 44 evidence to support the use of age and population-specific templates in human brain mapping 45 studies. These templates, with corresponding atlases and tools, are publicly available on the 46 NIMHANS and AFNI websites. 47Keywords: MRI, brain template, brain atlases, maximum probability map 48 1 Introduction 49The shape, size and volume of the human brain is highly variable across individuals, as well as across 50 age, gender and geographical location or ethnicity. This fact is of prime importance in neuroimaging 51 group studies, where the brains of all subjects are typically aligned to a single template space for 52 data analysis and for the reporting of findings where analogous anatomical structures are mapped 53 on to the same coordinate location across the subjects. A brain template provides a standard 54 3D coordinate frame to combine and/or compare data from many subjects, across different imaging 55 modalities, structural or functional and even different laboratories around the world. The properties 56 of the template (size, shape, tissue contrast, etc.) directly affect the quality of alignment. 57An early brai...

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BRAHMA: Population specific T1, T2, and FLAIR weighted brain templates and their impact in structural and functional imaging studies

Cited by 16 publications

References 67 publications

A series of five population‐specific Indian brain templates and atlases spanning ages 6–60 years

A series of five population‐specific Indian brain templates and atlases spanning ages 6–60 years

In vivo Population Averaged Stereotaxic T2w MRI Brain Template for the Adult Yucatan Micropig

A series of five population-specific Indian brain templates and atlases spanning ages 6 to 60 years

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