Batch Processing of CAT12 segmentation

1

Dear all,
Is there any way to 'batch' run CAT12 segmentation?
After add all T1 images to subjects, The CAT12 segmentation is disabled in pipeline tab, and only run one by one in the anatomy tab.

2

Hi @ipsych,

One way to do this is by creating a script to call the CAT12 process for each subject.

  1. Empty the Process1 tab
  2. Select the process Import > Import anatomy > Segment MRI with CAT12
  3. Do not run the pipeline, select the menu iconCondition > Generate .m script instead. It saves a new .m file and opens it in the Matlab editor.
  4. This script runs CAT12 segmentation on 1 subject. Modify the script to run the process in a for loop for each of your subjects.

More information on Scripting in Brainstorm here:
https://neuroimage.usc.edu/brainstorm/Tutorials/Scripting

Best,
Raymundo

3

Thanks for kind advice.

I just found the issue was dealt as an example in the scripting tutorial.
https://neuroimage.usc.edu/brainstorm/Tutorials/Scripting#Loop_over_subjects