skull and scalp


This stage creates mesh surface representations of the brain, inner and outer skulls, and the scalp.


  1. Initialization

  2. Segment Scalp

  3. Segment Outer

  4. Skull Segment Inner

  5. Skull Generate Surfaces

Command-Line Usage

skullfinder: generates a label file to segment brain, scalp, inner and outer skull

usage: skullfinder -i input -o output -m mask [optional settings]

example: skullfinder -i subj.nii.gz -o subj.skull.label.nii.gz -m subj.mask.nii.gz –scalplabel subj.scalp.label.nii.gz

Required Settings:
Flags Description
-i <input filename> input MRI volume
-o <output filename> output multi-colored label volume segmenting brain, scalp, inner skull & outer skull
-m <mask filename> input whole brain mask volume
Optional Settings:
Flags Description
-g debug
-v <level> verbosity [default: 0]
-l <lower threshold> lower threshold for segmentation [default: 0]
-u <upper threshold> upper threshold for segmentation [default: 0]
-s surface_prefix if specified, generate surface files
--bglabel <background_label> background label value (0-225) [default: 0]
--scalplabel <scalp_label> scalp label value (0-255) [default: 16]
--skulllabel <skull_label> skull label value (0-255) [default: 17]
--spacelabel <space_label> space label value (0-255) [default: 18]
--brainlabel <brain_label> brain label value (0-255) [default: 19]
--finalOpening perform a final opening operation on the scalp mask

Example Result

Output Files

If “save output of each stage automatically” is checked on the Cortical Surface Extraction dialog, the following files are generated (where filename_prefix is the filename of the MRI scan without the file extension, e.g. “testsubj” for the file “testsubj.nii”):

Filename Contents
fileprefix.skull.label.nii.gz Label volume of brain and space
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

Restore from Previous Session

If BrainSuite was interrupted while performing this stage or to change the parameters for this stage and rerun after fully processing a scan, click “Restore From Previous…” on the bottom of this stage’s dialog box and load the original MRI scan. BrainSuite will automatically load all of the files generated in previous stages, allowing processing to restart from this intermediate stage.