I’m trying to run the “Skull and scalp” part of the Cortical Surface Extraction after the skull stripping via the command line. According to the online guide ( http://brainsuite.org/processing/surfaceextraction/skull-and-scalp/ ), I can specify an upper and a lower threshold (-l and -u). In the GUI, however, there’s a skull and a scalp threshold. Are these 2 pairs of thresholds the same? And what do the “label values” (0-255) in the command line guide refer to?
When I run skullfinder, it does not automatically output the .dfs surface file. Is there a way to create the surface files directly via the command line?
Skull threshold is the lower threshold hold and scalp threshold is the upper threshold.
The label values represent an arbitrary numerical value that a specified voxel will take on. For example, any voxel that has a label value of 16 will be considered/labeled as scalp in BrainSuite. You have the option to set this integer value.
To save out the surface files, you have to run the Skull and scalp step in the Cortical Surface Extraction Sequence dialog (Cortex -> Cortical Surface Extraction Sequence dialog). Make sure that the “save output of each stage automatically” box is checked (autosave is default). If you already have the structural file and brain mask (fileprefix.mask.nii.gz) loaded, then you can uncheck the Skull stripping step and just run the the Skull and scalp stage.
You can also run this via command line, with an additional -s flag to have the surface outputs as described here.