BrainSuite

Batch Skull Stripping

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    • August 22, 2017 at 12:47 am #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?

    • August 28, 2017 at 9:13 am #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

    • August 28, 2017 at 10:42 am #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.

    • August 29, 2017 at 10:43 pm #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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