Correction Split Brain from Brain Mask
Correction Split Brain from Brain MaskGuide to overcome Ana Split Brain From Brain Mask problems
The hemisphere/cerebellum splitting procedure failed. Usually, the problem occurs at the interface between hemisphere and cerebellum. Try one by one the variants provided here. The only difference between all of them is the threshold used to define the white matter mask. If you are lucky, you may get a better split. Otherwise, chech the behaviour of the bias correction result at the level of the cerebellum, and try to trigger it again using different parameters.
Another source of problem is limited field of view in Z. If one part of the cerebellum is missing, the algorithm can not find a seed for the cerebellum. In that case, try to modify some of the parameters of Vip Split Brain, especially the minimal size of the connected component taken into account.
NB: if you work with monkey brains, you may have to use the command line without template.
If nothing solve your problems, you will have to perform some manual corrections with Anatomist drawing's capacities: Label volume editor (you can use a shortcut to this treatment through a dedicated icon in brainVISA interface).
mri_corrected: T1 MRI Bias Corrected ( input )
variant: Choice ( input )
split_mask: Split Brain Mask ( output )
histo_analysis: Histo Analysis ( input )
brain_mask: T1 Brain Mask ( input )
Use_template: Boolean ( input )
split_template: Hemispheres Template ( optional, input )
Commissure_coordinates: Commissure coordinates ( optional, input )
Toolbox : Morphologist
User level : 0
Identifier :
AnaSplitBrainFromBrainMaskCorrectionSupported file formats :
mri_corrected :GIS image, GIS imagesplit_mask :GIS image, GIS imagehisto_analysis :Histo Analysis, Histo Analysisbrain_mask :GIS image, GIS imagesplit_template :GIS image, GIS imageCommissure_coordinates :Commissure coordinates, Commissure coordinates