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Whole Brain Segmentation
v1.0. Cost per launch: 23.64 USD
1,633 analyzes performed.
1 votes

Other from LAIMBIO - URJC


[en] Whole brain segmentation Segmentation of cortical and subcortical brain structures using FreeSurfer. Data analysis: FreeSurfer ( https://surfer.nmr.mgh.harvard.edu/ ) is a free software package developed at the Martinos Center for Biomedical Imaging which can be used for measuring various morphometric properties of the brain including cortical and sub-cortical regional volumes and cortical thickness. Starting with the good quality T1-weighted MR image volume, the first step in the FreeSurfer processing is to perform a motion correction, affine transformation (12 degrees of freedom) to Talairach image space, non-uniform intensity normalization for intensity inhomogeneity correction, and removal of non-brain tissues. The remaining brain image volume is intensity normalized to match the FreeSurfer atlas image intensity histogram, which is followed by a non-linear warping of the atlas brain image to subject brain image. Warped atlas brain image in the subject image space is utilized in atlas-based tissue segmentation, in labeling the subcortical structures, brain stem, cerebellum, and cerebral cortex. The next step in FreeSurfer is to generate topologically correct cortical surface representation per hemisphere. Cortical surface lies either at the WM/GM tissue interface or at the GM/CSF tissue interface. Each hemisphere's cortical surface representation is mapped automatically to a standard spherical coordinate system. Key components of the surface mapping include surface inflation with minimal metric distortion, projection to spherical coordinates, topology correction, and surface based warping to align anatomically homologous points. Mapping to the standard spherical coordinate system defined by FreeSurfer atlas brain allows for automated anatomical parcellation of cortex into gyral regions. Surface parcellation is then extended to GM volume, yielding parcellation of GM tissue sheet and regional cortical volumes. INPUTS: T1-weighted 3D volume: Structural image to be segmented. OUTPUTS: Subcortical segmentation: Complete segmentation of the subcortical structures. Each structure is labeled with a unique color/number distinction. Cortical Segmentation: This segmentation shows the same subcortical structures that are labeled in the subcortical segmentation, but uses the cortical parcellation labels aroun the cortex. Normalized T1: Intensity normalized volume. [es] Volumetría total del cerebro Volumetría cortical y subcortical de las estructuras cerebrales usando FreeSurfer. Análisis de los datos (inglés): FreeSurfer (https://surfer.nmr.mgh.harvard.edu/) is a free software package developed at the Martinos Center for Biomedical Imaging which can be used for measuring various morphometric properties of the brain including cortical and sub-cortical regional volumes and cortical thickness. Starting with the good quality T1-weighted MR image volume, the first step in the FreeSurfer processing is to perform a motion correction, affine transformation (12 degrees of freedom) to Talairach image space, non-uniform intensity normalization for intensity inhomogeneity correction, and removal of non-brain tissues. The remaining brain image volume is intensity normalized to match the FreeSurfer atlas image intensity histogram, which is followed by a non-linear warping of the atlas brain image to subject brain image. Warped atlas brain image in the subject image space is utilized in atlas-based tissue segmentation, in labeling the subcortical structures, brain stem, cerebellum, and cerebral cortex. The next step in FreeSurfer is to generate topologically correct cortical surface representation per hemisphere. Cortical surface lies either at the WM/GM tissue interface or at the GM/CSF tissue interface. Each hemisphere's cortical surface representation is mapped automatically to a standard spherical coordinate system. Key components of the surface mapping include surface inflation with minimal metric distortion, projection to spherical coordinates, topology correction, and surface based warping to align anatomically homologous points. Mapping to the standard spherical coordinate system defined by FreeSurfer atlas brain allows for automated anatomical parcellation of cortex into gyral regions. Surface parcellation is then extended to GM volume, yielding parcellation of GM tissue sheet and regional cortical volumes. ENTRADAS: T1-weighted 3D volume: Imagen anatomica a segmentar. Volumen 3D T1 de Resonancia Magnética. SALIDAS: Report: Informe en PDF con los valores volumétricos de las estructuras. Subcortical segmentation: Volumen 3D con la segmentación completa de las estructuras subcorticales. Casa estructura está etiquetada con un color y número. Cortical Segmentation: Volumen 3D con la segmentación igual que la anterior pero usando las etiquetas de la parcelación cortical alrededor del cortex. Normalized T1: Volumen original normalizado en intensidad.

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