Segmentation.SpecializedForeground masking (BRAINS)This program is used to create a mask over the most prominant forground region in an image. This is accomplished via a combination of otsu thresholding and a closing operation.
5.8.0https://slicer.readthedocs.io/en/latest/user_guide/modules/brainsroiauto.htmlhttps://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txtHans J. Johnson, hans-johnson -at- uiowa.edu, http://www.psychiatry.uiowa.eduHans Johnson(1,3,4); Kent Williams(1); Gregory Harris(1), Vincent Magnotta(1,2,3); Andriy Fedorov(5), fedorov -at- bwh.harvard.edu (Slicer integration); (1=University of Iowa Department of Psychiatry, 2=University of Iowa Department of Radiology, 3=University of Iowa Department of Biomedical Engineering, 4=University of Iowa Department of Electrical and Computer Engineering, 5=Surgical Planning Lab, Harvard) Input/output parametersinputVolumeinputVolumeThe input image for finding the largest region filled mask.inputoutputROIMaskVolumeoutputROIMaskVolumeThe ROI automatically found from the input image.outputoutputVolumeoutputVolumeThe inputVolume with optional [maskOutput|cropOutput] to the region of the brain mask.outputmaskOutputmaskOutputThe inputVolume multiplied by the ROI mask.truecropOutputcropOutputThe inputVolume cropped to the region of the ROI mask.falseotsuPercentileThresholdotsuPercentileThresholdParameter to the Otsu threshold algorithm.0.01thresholdCorrectionFactorthresholdCorrectionFactorA factor to scale the Otsu algorithm's result threshold, in case clipping mangles the image.1.0closingSizeclosingSizeThe Closing Size (in millimeters) for largest connected filled mask. This value is divided by image spacing and rounded to the next largest voxel number.9.0ROIAutoDilateSizeROIAutoDilateSizeThis flag is only relavent when using ROIAUTO mode for initializing masks. It defines the final dilation size to capture a bit of background outside the tissue region. At setting of 10mm has been shown to help regularize a BSpline registration type so that there is some background constraints to match the edges of the head better.0.0outputVolumePixelTypeoutputVolumePixelTypeThe output image Pixel Type is the scalar datatype for representation of the Output Volume.shortfloatshortushortintuintucharnumberOfThreadsnumberOfThreadsExplicitly specify the maximum number of threads to use.-1