Skull and Scalp Segmentation

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

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

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

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

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.