mouse spinal cord atlas (allen brain atlas)  (Allen Institute for Brain Science)

Journal: Brain

Article Title: Multiple sclerosis lesions in motor tracts from brain to cervical cord: spatial distribution and correlation with disability

doi: 10.1093/brain/awaa162

Figure Lengend Snippet: Processing pipeline. Brain data processing: (1) semi-automatic lesion segmentation on 3D T2-FLAIR or axial T2-weighted images (when 3D T2-FLAIR was not available); (2a) intra-subject linear registration between T2-FLAIR and T1-weighted images; (2b) Affine and non-linear registration between T1-weighted images and the T1 ICBM 1 mm isotropic template space; and (3) quantification of lesion volume fraction based on brain and brainstem CST atlases. Spinal cord data processing: (1) manual lesion segmentation on axial T2*-weighted images; (2) slice-wise non-linear registration to the PAM50 template; and (3) Quantification of lesion volume fraction based on a spinal cord CST atlas. To create the lesion frequency maps, brain and spinal cord lesion masks were averaged in the ICBM and PAM50 space, respectively.

Article Snippet: Spinal cord data processing: (1) manual lesion segmentation on axial T 2 *-weighted images; (2) slice-wise non-linear registration to the PAM50 template; and (3) Quantification of lesion volume fraction based on a spinal cord CST atlas.

Techniques:

Journal: Brain

Article Title: Multiple sclerosis lesions in motor tracts from brain to cervical cord: spatial distribution and correlation with disability

doi: 10.1093/brain/awaa162

Figure Lengend Snippet: Lesion frequency in the brain, brainstem and cervical spinal cord. (A) Lesion frequency maps for the whole cohort and for each disease phenotype. The CST are indicated in red contour. (B) Lesion frequency along the CST for each phenotype subcohort. For each axial slice (1-mm slice thickness), the CST lesion frequency median and interquartile range are represented by a solid line and shaded region, respectively. The CST segments are demarcated by dashed vertical lines. When interpreting this graph, it is important to keep in mind that the lesion frequencies are normalized by the CST volume.

Article Snippet: Spinal cord data processing: (1) manual lesion segmentation on axial T 2 *-weighted images; (2) slice-wise non-linear registration to the PAM50 template; and (3) Quantification of lesion volume fraction based on a spinal cord CST atlas.

Techniques:

Journal: Brain

Article Title: Multiple sclerosis lesions in motor tracts from brain to cervical cord: spatial distribution and correlation with disability

doi: 10.1093/brain/awaa162

Figure Lengend Snippet: Absolute and normalized lesion volumes for each phenotype, measured in the whole CST, in the brain, brainstem and spinal cord portion of the CST. ***P < 0.0001, **P < 0.001, *P < 0.05. For clarity, only significant differences between relapsing-remitting and progressive phenotypes are reported, and not between clinically isolated syndrome and other phenotypes. For each box plot, the median is indicated as a thick horizontal line and the interquartile range as a rectangle. The horizontal bar at both extremities of the whiskers indicates the 5th and 95th percentiles. The circles indicate outliers.

Article Snippet: Spinal cord data processing: (1) manual lesion segmentation on axial T 2 *-weighted images; (2) slice-wise non-linear registration to the PAM50 template; and (3) Quantification of lesion volume fraction based on a spinal cord CST atlas.

Techniques: Isolation

Journal: Brain

Article Title: Multiple sclerosis lesions in motor tracts from brain to cervical cord: spatial distribution and correlation with disability

doi: 10.1093/brain/awaa162

Figure Lengend Snippet: Frequency of multiple sclerosis lesions in the brain, brainstem and spinal cord for patients grouped by pyramidal functional system score. (A) Lesion frequency maps. Pyramidal functional system score (FSS) subgroups: low pyramidal functional system score (0), medium pyramidal functional system score (1–2), high pyramidal functional system score (≥3). The CST is indicated in red contour. (B) Lesion frequency along the CST for each pyramidal functional system score subcohort. For each axial slice (1-mm slice thickness), the CST lesion frequency median and interquartile range are represented by a solid line and shaded region, respectively. The CST segments are demarcated by dashed vertical lines. Pyramidal functional system score (py FSS) subgroups: low pyramidal functional system score (0), medium pyramidal functional system score (1–2), high pyramidal functional system score (≥3). When interpreting this graph, it is important to note that the lesion frequencies are normalized by the CST volume.

Article Snippet: Spinal cord data processing: (1) manual lesion segmentation on axial T 2 *-weighted images; (2) slice-wise non-linear registration to the PAM50 template; and (3) Quantification of lesion volume fraction based on a spinal cord CST atlas.

Techniques: Functional Assay

Journal: Brain

Article Title: Multiple sclerosis lesions in motor tracts from brain to cervical cord: spatial distribution and correlation with disability

doi: 10.1093/brain/awaa162

Figure Lengend Snippet: Multivariate linear regression of EDSS, pyramidal functional system score, 9HPT and TWT

Article Snippet: Spinal cord data processing: (1) manual lesion segmentation on axial T 2 *-weighted images; (2) slice-wise non-linear registration to the PAM50 template; and (3) Quantification of lesion volume fraction based on a spinal cord CST atlas.

Techniques: Functional Assay