Command Line: Cerebrum Labeling

Forums Forums Cortical Surface Extraction Command Line: Cerebrum Labeling

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    • #363
      wwu94
      Participant

      Hi,

      I am using BrainSuite command line version under ssh server Linux environment:

      I encountered the following problem when I try to perform Cerebrum labeling using the default atlas: brainsuite.icbm452.lpi.v08a.img and brainsuite.icbm452.v15a.label.img:

      Initializing brain volume
      Performing linear alignment of atlas brain to subject brain
      Performing warp alignment (order=5) of atlas brain to subject brain
      do_align_warp.c: 213:
      Problem with file ./brainLETN3m/scale.init
      The specified file does not exist. (AIR_NO_FILE_READ_ERROR)
      warp process failed.
      error during warping
      unable to finish making label output.

      I am not sure where the problem is, but the process was working fine in the GUI version on my own computer.

      Thanks for helping!

    • #364
      David Shattuck
      Keymaster

      Hello –

      Can you provide the specific command line call that you are making, including all arguments?

      If that stage works in the GUI, the best thing to do is to use the cortical_extraction.cmd script. It is configured to have settings that match those in the GUI, and will produce identical results.

      thanks,
      David Shattuck

      • #365
        wwu94
        Participant

        Hi,

        Thanks for replying!

        Here is the code I used:
        ## DIR is where I put all the skull-stripped volume (output from skull-stripping function).
        ## of and of2 are just formatted output file names.
        for f in “$DIR”/*_mri.nii.gz
        do
        /home/share/BrainSuite16a/bin/cerebro -i “$f” –atlas “/home/share/BrainSuite16a/atlas/brainsuite.icbm452.lpi.v08a.img” –atlaslabels “/home/share/BrainSuite16a/atlas/brainsuite.icbm452.v15a.label.img” -l “$DIR/$of” -o “$DIR/$of2”

        For cortical_extraction.cmd: can that be executed in Linux environment? I thought it’s for windows platform. If it can, can you be a little more specific on that?

        Thanks a lot for helping!

    • #549
      David Shattuck
      Keymaster

      Hello –

      There is also cortical_extraction.sh, which can be run from bash on Mac or Linux. It sets all of the parameters to be the same as the GUI. If necessary, you can copy it and edit it if you need to make any changes. If you do edit it, then you will want to make sure that BrainSuiteDir is set to the installation path. If it is not set, then the script will try to find the files based on location of the script.

      thanks,
      David

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