Raw data files not displayed after loading existing protocol

Bugs
1

Environment:

  • Brainstorm version: brainstorm_251018.zip

  • MATLAB version: R2023b (Academic use)

  • OS: macOS with M4 chip (Apple Silicon)

  • Computer: Fresh installation on new Mac

Background: I have a file protocol that was created in an older version of Brainstorm. I exported/zipped this protocol and am now trying to use it on a new computer with a fresh Brainstorm installation.

Detailed description of the problem:

Step 1: What I did

  • Installed MATLAB R2023b with full license through my university

  • Downloaded and installed Brainstorm (latest version from October 16, 2025)

  • Configured MATLAB Runtime R2023b and set LIBRARY_PATH as instructed

  • Successfully launched Brainstorm from MATLAB

Step 2: Loading the protocol

  • Extracted my file protocol ZIP file to my Documents folder

  • The extracted folder contains multiple subject folders: Subject 1, Subject 2, Subject 3, etc.

  • Inside each subject folder, I can see in Finder that there are subfolders with data files (anatomy files, channel files, data files, etc.)

  • Used File → Load protocol in Brainstorm and selected the file folder

  • Brainstorm prompted: "Warning: You are running a newer version of Brainstorm. Some modifications have to be performed on your database. Update database now?"

  • I clicked "Yes"

Step 3: The problem –> After the database update completes:

  • The protocol “my file” appears in the left panel of Brainstorm

  • I can see all the subject folders listed (Subject 1, Subject 2, Subject 3, etc.)

  • I can expand each subject folder

  • Under each subject, I see "Default anatomy"

    BUT: There are no data files visible anywhere

What I expect to see but don't:

  • Raw data links/files under each subject

  • Processed data files

What I actually see:

  • Just the subject names and "Default anatomy"

  • Empty space where the data should be

  • The interface looks like the protocol has subjects but no imported data

Visual description:

StroopTask (anatomy)

├─ Default anatomy

├─ Subject 1

│ └─ Default anatomy [nothing below this]

├─ Subject 2

│ └─ Default anatomy [nothing below this]

└─ [other subjects, same pattern]

What I verified:

  • The original protocol folder on disk DOES contain all the data files (I can see them in Finder)

  • The folder structure looks complete with anat/, data/, and other subfolders

  • File sizes indicate data is present (not empty folders)

What I've tried:

  1. Clicking "No" on database update: Protocol becomes completely inaccessible with error "protocol directory not found"

  2. File → Load protocol multiple times: Same result each time

  3. Creating a fresh protocol and trying to import the anatomy folders: Shows subjects but still no data files

  4. Restarting Brainstorm: Same issue persists

My questions:

  1. Is there a known compatibility issue when loading protocols created in older Brainstorm versions?

  2. Does the database update process potentially fail to properly index/display existing data files?

  3. Is there a log file I can check to see what's happening during the database update?

  4. Should I try a different approach to import this existing protocol?

  5. Do I need to downgrade Brainstorm to match whatever version created this protocol originally?

Additional context: This is my first time setting up Brainstorm on Apple Silicon (M4 chip). I'm not sure if there are any special considerations for this architecture that might be causing issues.

Any help would be greatly appreciated! I have all my analysis work in this protocol and need to access the data

Thank you,
Ana

2

If installing the full version of Matlab, it is possible to run Brainstorm from source code, rather than the standalone (binary) version.

It seems the dataset is being explored in the Anatomy view.
The shared tree, suggests that the Default anatomy is being used for the subjects. This is often the case for datasets wherer there is not individual anatomy files (MRI and surfaces for each subject.

In all our loading protocols created with older Brainstorm versions get correctly updated to the newer versions.

Last database update, added an extra field in headmodel files (commit b00f3d0).
It does not modify modify the structure of the database, nor add or delete files in the protocol.

Any relevant information is printed out in the command window.

Try what was suggested in:

That is not required, as Brainstorm is able to identify the DB version that was used, and make the necessary updates in the DB.

  • How did you create the .zip file that contains the protocol files?

  • Which is the value of the DbVersion* variable stored in the file PROTOCOL_ZIP/data/protocol.mat

  • When loading the protocol, do you see any message printed?

  • What is it shown in the Functional data view?

    view_functional.gif
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