[David Shattuck]

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

[wwu94]

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!

[David Shattuck]

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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