Importing MRI segmentation by CAT12

[Taiziliulong]

Hi everyone, I'm working on source analysis of children/adolescents EEG. I have run the segmentation process of a public template in Brainstorm using CAT12, and I got the following files in the directory **\brainstorm_db\Protocol01\anat\Subject05.

Then I tried to import this anatomy folder as Subject07's anatomy (since they used the same template). However, I could only get the T1 file and the headmask.

Is there a way I can import the whole anatomy folder of Subject05 into Subject07?

[tmedani]

If the segmentation outputs are still in your temporary folder, you can import them by right-clicking on a subject and then importing anatomy.

The other fast option is to duplicate the subject 05 and the rename it subject 07,
to do that, right-click on the subject> file> duplicate subject.

[Taiziliulong]

Thank you for your quick reply I found that at the end of the segmentation by CAT12, the temporary folder is deleted. And after I recovered the file from the recycle bin and tried to import it, the following error occurred. It seems that something is missing.

So I have also tried the second way, which seems convenient. After the duplication, I proceeded with BEM surfaces generation and source computation. The procedures went without error. But I was confused. Is it normal to have two BEM head, outerskull, and inner skull files in one subject?

[Raymundo.Cassani]

Hi @Taiziliulong,

@Taiziliulong

Is there a way I can import the whole anatomy folder of Subject05 into Subject07?

Yes, you can create a Template anatomy from the anatomy of Subject05, and use this template for Subject07.

Check this link:
https://neuroimage.usc.edu/brainstorm/Tutorials/DefaultAnatomy#Create_new_templates

1. Once you have imported the anatomy for Subject05,
   right-click on the subject node > Use template > Create new template and give it a name

2. Create Subject07, then
   right-click on the subject node > Use template and select the created new template

• By doing as above Subject07 will have an anatomy that is the copy of Subject05. But changes do not propagate. E.g. deleting a surfaces in one Subject will not delete the same surface on the other Subject
• This new template is saved in the user directory, so it will be available for any other Protocol.
• If ALL the subjects in the same protocol will use the same Template, when creating the Protocol, set the Default anatomy to use the created template, then all the users to use the Default anatomy. By doing so, all subjects will use the same anatomy files, i.e., if a surface is deleted on the Default anatomy this surface will not be available for any Subject.

Alternatively, you could duplicate Subject07 and rename the copy to Subject05, as mentioned:

Importing MRI segmentation by CAT12

If the segmentation outputs are still in your temporary folder, you can import them by right-clicking on a subject and then importing anatomy. The other fast option is to duplicate the subject 05 and the rename it subject 07, to do that, right-click on the subject> file> duplicate subject.

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@Taiziliulong

Then I tried to import this anatomy folder as Subject07's anatomy (since they used the same template). However, I could only get the T1 file and the headmask.

As you can see in the Import anatomy folder... window, there is no option Brainstorm anatomy.
So by selecting the MRI, it will just run CAT12 for MRI already in the Brainstorm database. This seems to be the origin of the troubles reported in: Importing MRI segmentation by CAT12 - #3 by Taiziliulong

[Taiziliulong]

Thank you so much! The way of setting a default template solved my problem perfectly.