sMRI Acquisition and Modalities

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course_flow

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MR_relax

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relax_tissue_contrast)

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T1

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T2

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mprage

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kspace

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nilearn_T1

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nilearn_T2

sMRI Clean-up

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course_flow

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  • Acquired T1w image (b) Estimated the bias field which can then be used to “correct” the image. (c) Bias field viewed as a surface to show the low frequency modulation. N4_bias

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    bias_correction

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    nilearn_bias_orig

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    nilearn_bias_corr

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    ANTs_brain_extract

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    FSL_brain_extract

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    nilearn_brain_orig

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    nilearn_brain_extract

    sMRI Spatial Normalization

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    course_flow

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    slicer_coordinate_systems

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    Drawing

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    MNI_spaces

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    mni_icbm152

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    registration_cartoon

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    rigid_process

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    nonlinear_deform_process

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    nilearn_reg

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    subject_vs_ref_space

    sMRI Segmentation and Parcellation

    Figure 1

    course_flow

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    Brain tissue types

    Figure 3

    Brain atrophy due to Alzheimer's or severe multiple sclerosis diseaseThis image is Copyright © My-MS.org and falls under Image License D defined under the Image License section of the My-MS.org Disclaimer page.

    Figure 4

    Axial slice of the T1 data (after skull-stripping)

    Figure 5

    Histogram of the T1 volume data, all tissues together

    Figure 6

    Tissue classes overlayed on the T1 data

    Figure 7

    Histogram of the T1 volume data, one distribution per tissue

    Figure 8

    GM probability map

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    Delineation of GM and WM

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    Delineation of GM and WM

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    Pial mesh from surface segmentation

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    WM mesh from surface segmentation

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    WM mesh from surface segmentation

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    AAL atlas

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    ROI from the AAL atlas

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    Left hemisphere of the Destrieux surface atlas

    Figure 17

    ROI of the Destrieux surface atlas

    sMRI Quality Control

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    course_flow

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    HC_and_CB_MAGeT

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    Drawing

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    t1_mri_visual_QC

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    alignment_mismatched_colormix_visualQC

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    cortical_zoomed_in

    sMRI Statistical Analysis

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    course_flow

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    Caudate nucleus from Freesurfer segmentation

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    Cortical thickness visualization for a given subject

    Figure 4

    Group cortical thickness boxplot

    Figure 5

    Example of cortical thickness variation with age in an ROI

    Figure 6

    Cortical thickness vs age - p values

    Figure 7

    Cortical thickness vs age - adjusted R squared

    Figure 8

    Cortical thickness vs age - surface t values on left hemi

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    Cortical thickness vs age - surface t values on right hemi

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    VBM template creation

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    VBM template creation

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    VBM mean warped maps

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    VBM mean warped maps

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    VBM mean warped maps

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    VBM mean warped maps

    sMRI Analysis: Reproducibility Considerations

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    course_flow

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    Drawing