average FreeSurfer Volumes

Explore the various atlas, mask and processed structural images obtained from the FreeSurfer cortical morphometrics and reconstruction pipeline.

The volumetric and surface atlases are automatically loaded unto the T1 image. You can select other parcellation schemes and volumes from the File menu.

You can show/hide volumes by clicking on one of the tiles on the top right of the image viewer. See the table below for included files.

Hints) Sometimes a volume does not load with correct brightness/contrast values. You can adjust these by right clicking, holding control and dragging across the image. Use spacebar to cycle through different image views. Scrolling through slices is faster if you hide other overlays.

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wmparc

Image Filename Description
T1 Weighted Siemens MPRAGE T1 High resolution (1x1x1mm voxel size) structural image
Skull-stripped Brain Mask brainmask Automated stripping of skull, neck and non-brain tissue used for all subsequent processing. Manual edits to skull stripping errors will appear as dark blue
White Matter Tissue Probability Mask wm Automatically generated tissue probability map of the white matter
Volumetric Subcortical Segmentation aseg Automatic image segmentation of subcortical structures obtained with a probabilistic classifier trained on a manually labeled dataset.
Cortical Parcels + Subcortical Segmentation aparc_aseg Cortical parcellation labels obtained from the 2006 Deskian-Killiany atlas that are transformed into volume space and superimposed on the volumetric labels
Volumetric Deskian Killiany Atlas aparc_DKTatlas_aseg Just the surface labels from the 2006 Deskian-Killiany atlas
Volumetric Cortical + Subcortical Segmentation aparc_a2009s_aseg The 2009 Destriuex Atlas, a finer grained surface parcellation.
White Matter Parcellation wmparc Atlas of the white matter obtained by labeling voxels with the closest cortical parcel