Hi everyone,
I’m working on a script for my project where I need to extract several surfaces using different thresholds in Brainstorm. While I can successfully perform this task using the GUI, I encounter some issues when trying to implement it in a script.
To give some context, I’ve included images showing the steps I follow in the GUI (Untitled 1-5). The general process involves importing the MRI, normalizing it using SPM, and then extracting the head surface.
I used the pipeline code generator to create the script (attached as code.jpeg). However, I'm facing one key issue: when trying to generate the head surface through the script, there's no option for background thresholding like there is in the GUI (see Untitled 6 image).
I’d appreciate any advice on how to add the background thresholding to my script. Also, if you notice any other important steps I might have missed when translating the GUI process into the script, please let me know.
Thank you in advance!
Best,
Reza