Batch Skull Stripping

Forums Forums Cortical Surface Extraction Batch Skull Stripping

This topic contains 3 replies, has 3 voices, and was last updated by  3qSB2x 2 years, 7 months ago.

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  • #828

    3qSB2x
    Participant

    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?

  • #832

    todflak
    Participant

    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!
    -Tod

  • #835

    Anand Joshi
    Moderator

    The MAC and Linux versions of BrainSuite17a have all the binaries included. Would you be able to use them by any chance? In the meantime we will check about the Windows build.

  • #842

    3qSB2x
    Participant

    I did it with the gui now. Took me some time but you know instantly if it worked and can adjust the mask. Would still be nice to have the files in the new version. Thanks!

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