How to multiple input nii file segmentation through CAT12

Discussions
1

Dear Brainstorm Team,

I am currently working with 782 MRI images in .nii.gz format and using CAT12-based segmentation methods. However, I find it challenging to repeatedly input each image into the protocol manually. I would like to automate this process to handle multiple inputs efficiently.

While I have referred to the following links:

  1. Scripting Tutorial
  2. Pipeline Editor Tutorial
  3. Loop over subjects

I am having difficulty understanding how to implement this for my case. Could you provide guidance or resources for scripting or using the GUI for this purpose?

Best regards,
LCY

2

Were you able to generate one script for one subject?

It should be straightforward afterward, once you have the script for one subject you can add a for loop and go over all your subjects.

3

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Thank you for reply to my question.

This is my brainstorm UI in the matlab.

How to make the new script in the subject?

4

You can open the process tab,
Click on the Run button, then select Import> Anatomy > Segment with Cat12, and then select the subject you want to segment.

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From this panel, you can generate the associated script for the selected subject,
and then change the script to loop over all your subjects.

5

Thank you tmednai we solved this problem

1 Like
6

:sunglasses:
It's great to hear it; thank you for the feedback!