I want to do skull stripping on various mri volumes the exact way the first stage in the “Cortical Surface Extraction Sequence” – Tool does. Especially I like to use the “automate parameter selection” feature (which seems to be new in 2017 version) because this seems to work very well on my data.
I know there is this script “cortical_extraction” for such a purpose. Problem is in Version 17a the bin folder is reduced to only some files. Can’t even find bse.exe in it.
Batch extraction works in version 16a1 but here I don’t know how I can use the automatic parameter selction via script.
Is there any further information available on batch skull stripping?
I have just posted a similar question.
Have you had any resolution of your question?
I’m wondering if we need to download the “BrainSuite GUI and command line tools [ 5.5 MB]” and build the command-line tools ourselves. Either that, or someone forgot to package the command line tools in the latest release!