CSE: Output Files

In the following, fileprefix is the MRI file’s prefix (e.g. “brainsuite_subj1” for the file “brainsuite_subj1.nii.gz”).

Skull-Stripping
Filename Description
fileprefix.mask.nii.gz Mask of entire brain (cerebrum + cerebellum + brainstem)
fileprefix.bse.nii.gz Skull-stripped MRI image
Skull and Scalp
Filename Description
fileprefix.brain.dfs Rough surface of brain (cerebrum + cerebellum + brainstem)
fileprefix.inner_skull.dfs Surface representation of inner skull
fileprefix.outer_skull.dfs Surface representation of outer skull
fileprefix.scalp.dfs Surface representation of scalp
Bias-Field Correction
Filename Description
fileprefix.bfc.nii.gz Skull-stripped image with bias-field correction applied
Tissue Classification
Filename Description
fileprefix.pvc.frac.nii.gz Label volume
fileprefix.pvc.label.nii.gz Label volume of tissue types. Contains labels for white matter, grey matter, CSF, and combinations of each.
Cerebrum Labeling
Filename Description
fileprefix.air File generated by AIR describing the transformations required for linear registration.
fileprefix.warp File generated by AIR describing the transformations requried for nonlinear (warp) registration.
fileprefix.hemi.label.nii.gz Label volume with left and right cerebrum, cerebellum, and ventricles/diencephalon.
fileprefix.cerebrum.mask.nii.gz Mask of the cerebrum for original scan
Identify Inner Cortical Mask
Filename Description
fileprefix.init.cortex.mask.nii.gz Mask representing the inner cortical boundary (boundary between white matter and cortical grey matter).
Scrub Mask
Filename Description
fileprefix.cortex.scrubbed.mask.nii.gz Inner cortical boundary mask, with small pits and bumps removed.
Topology Correction
Filename Description
fileprefix.cortex.tca.mask.nii.gz Scrubbed inner cortical boundary mask with topological corrections.
Wisp Removal
Filename Description
fileprefix.cortex.dewisp.mask.nii.gz Topologically-correct scrubbed inner cortical boundary mask with wispy structures removed.
Inner Cortical Surface
Filename Description
fileprefix.inner.cortex.dfs Surface representing the boundary between white matter and cortical grey matter. Provides the foundation for the generation of the pial surface.
Pial Surface
Filename Description
fileprefix.pial.cortex.dfs Pial surface of the subject’s brain
Split Hemispheres
Filename Description
fileprefix.left.inner.cortex.dfs Left hemisphere’s inner cortical boundary surface.
fileprefix.left.pial.cortex.dfs Left hemisphere’s pial surface.
fileprefix.right.inner.cortex.dfs Right hemisphere’s inner cortical boundary surface.
fileprefix.right.pial.cortex.dfs Right hemisphere’s pial surface.