Brainstorm Protocol Data not Opening after Updating Brainstorm

Bugs
1

Hello,

M Brainstorm updated to the 09/18/2025 version and now when I try to open one of my protocols it does not show any of the subject data folders. The other protocols included in my data base folder are showing up normally. The protocol folder is saved to my computer and I can see all the subject data folders there. Would it be possible for me to get the older version of brainstorm back, would that restore my data? Or does anyone know how I can get these subject data folders to load in brainstorm again?

When I try to reload the protocol it says “the input files do not exist anymore”. I do see that all the raw files are still saved on my computer though.

Thank you,

Karolina

brainstorm_and_protocol_data
brainstorm_and_protocol_data2338Ă—1426 110 KB

2

Before starting, make a backup of your protocol (StroopTask) folder, and store it outside of the Brainstorm database folder. With this done, follow theses steps:

  1. In the main Brainstorm window go to File > Delete protocol > Only detach from database
  2. Close Brainstorm and Matlab
  3. Delete the file /brainstorm_db/StroopTask/data/protocol.mat
  4. Start Brainstorm
  5. In the main window, go to File > Load protocol > Load from folder and select your protocol folder `/brainstorm_db/StroopTask``

With this Brainstorm will regenerate the contents of the protocol.mat file (used to fill in the database tree in the GUI) from all the files in the protocol.

Raw data files not displayed after loading existing protocol
3

Hi Raymundo,

Thank you for the reply. Unfortunately, after following the given steps, Brainstorm is still not working. When we load the file, we don’t see anything. I’m attaching a picture to show that:

IMG_0916.HEIC
IMG_0916.HEIC2268Ă—4032 2.13 MB

What else could we do?

Thank you in advance,
Ana

4

Did you get any message in the Matlab command window?

5

Hi again Raymundo,

This is what we’re getting in the MATLAB command

Screenshot 2025-10-15 115954
Screenshot 2025-10-15 1159541291Ă—379 11.4 KB

I was wondering if I could arrange a quick call to chat about this issue?

Thank you,
Ana

6

Is there a way to download the older version of brainstorm so we can open this protocol again? I tried looking in github but don’t know where the older version brainstorm files are.

7

Yes, you need to clone the repository at the commit of version you are looking for.
Is there are specific date you want to download?

8

I think the Aug 5 2025 version could have been the one we used last. Is there a specific file name that I should look for?

9

Check this link:
GitHub - brainstorm-tools/brainstorm3 at cf697e7e9c0eaf25110f10c4ce9b6b6a8f27380b

It is for Brainstorm 05-Aug-2025, go to the green Code button and Download ZIP.
This is a snapshot at that date.

  1. Make a copy of your protocol zip
  2. Check if you can load the protocol with this older version and if so, update Brainstorm to update the database as well.

Keep in mind that using older versions of rolling-release software such a Brainstorm defeats its purpose. By doing so, new features and improvements will be missed. Moreover, the longer you postpone updates, the more difficult may become to upgrade later.

1 Like
10

Thank you for sending the link. Do you know how to bypass this error?

matlab_error
matlab_error1188Ă—354 6.09 KB

11

This means the protocol you are trying to import has been already updated.

You can try to remove the ./data/protocol.mat file from the protocol files and try to import it