Z-score normalization choices

Discussions
1

Hello, Francois,

For evoked response analysis, I have calculated MNE source for each task condition for a subject and I need to do some Z-score normalization again baseline. I saw there’re multiple Z-score choices for source domain analysis in the recent version of brainstorm — “Z-score (static)” and “Z-score (dynamic)” in the “Standardize” tab, and “test: Z-score noise normalization” in the “Normalize” tab. What are the differences between these three choices?

Thanks,

Zhimin

2

Hi Zhimin:

They are equivalent: the dynamic z-score is actually a new and more efficient way of handling z-transformed data from the software side. The actual dynamic and static z-tranfsorms are identical. Eventually the static version will be removed from the distribution.

Cheers,

3

Hi Zhimin,

You shouldn’t have a process called “Test > Z-score noise normalization”, this is coming from an old version of Brainstorm. If you have this one, you probably have many other files that are going to cause some conflicts.
Please delete your current brainstorm3 folder and download the current version, instead of just unzipping it at the same place.

Another possibility is that you have several brainstorm versions in your static Matlab path. You should add any of the brainstorm folders in the static path. Edit you Matlab path, remove ALL the folders and subfolders including the braisntorm3 name, and save.
Then go to the brainstorm3 folder and type “brainstorm”.

Cheers,
Francois

4

Thank you very much, Sylvain and Francois. I’ll download the latest version then.

Zhimin

5

(don’t forget to delete the old one first)

6

Francois,

I downloaded the BST version from today but I still see that process called “Test > Z-score noise normalization”. How come?

Zhimin

7

Another file process_zscore is somewhere in your path, in your personal process folder ($HOME/.brainstorm/process), or you didn’t delete the previous brainstorm3 folder.

8

Oh, you are right, I forgot there’s that file in my $HOME/.brainstorm/process folder. I’ll delete that. Thanks.

Zhimin

9

I deleted that “process_zscore3.m” file in my personal process folder and no longer find that “Test > Z-score noise normalization” in the “Normalize” tab. Thank you very much.

Zhimin

10

Hi Zhimin,
The process_zscore3.m is a custom process that you use in your clinical pipeline. If you remove it from your .brainstorm folder you no longer have that process available to use. You should put is back if you intend to use it in your pipeline.

Beth

11

Ooops, sorry for giving you wrong directions…