Unable to reload the protocol

Renoald · December 3, 2025, 9:55pm

Hi team,
I’ve run into an urgent problem: after a MATLAB crash, my protocol no longer loads fully. The imaging data still loads, but all EEG data fails to load—only the “review raw file” items remain. Could you please advise on what I should do to recover or fix this? Thank you!

Additionally, I found that the data loads correctly when sorted by condition, but not when sorted by subjects.

protocol.mat (263.1 KB)
Here is the data protocol generate by brainstorm

Raymundo.Cassani · December 4, 2025, 3:45pm

Right-click on the top node in the Brainstorm database explorer, then on Reload

Check if there are any message in the Matlab command window

Renoald · December 4, 2025, 4:16pm

Thanks for your guidance. Below is the MATLAB Command Window output (apologies—my MATLAB language is set to Simplified Chinese):

警告: Cannot open anatomy file 'G:\brainstorm_db\Test_001\anat\01gaoyibo_2021ft\subjectimage_3DT1.mat'.

位置：db_parse_subject/io_getAnatomyInfo (第 273 行)
位置: db_parse_subject (第 157 行)
位置: db_parse_subject (第 138 行)
位置: db_load_subjects (第 125 行)
位置: db_reload_database (第 74 行)
位置: panel_protocols>ReloadNode (第 720 行)
位置: panel_protocols (第 46 行)
位置: tree_callbacks>@(h,ev)panel_protocols('ReloadNode',bstNodes(1)) (第 2723 行)
警告: Cannot open anatomy file
'G:\brainstorm_db\Test_001\anat\01gaoyibo_2021ft\subjectimage_second_post_seeg_spm_reslice_masked_spm_volct.mat'.
位置：db_parse_subject/io_getAnatomyInfo (第 273 行)
位置: db_parse_subject (第 157 行)
位置: db_parse_subject (第 138 行)
位置: db_load_subjects (第 125 行)
位置: db_reload_database (第 74 行)
位置: panel_protocols>ReloadNode (第 720 行)
位置: panel_protocols (第 46 行)
位置: tree_callbacks>@(h,ev)panel_protocols('ReloadNode',bstNodes(1)) (第 2723 行)
警告: Cannot open anatomy file 'G:\brainstorm_db\Test_001\anat\04liushuhan\subjectimage_251015_2142.mat'.
位置：db_parse_subject/io_getAnatomyInfo (第 273 行)
位置: db_parse_subject (第 157 行)
位置: db_parse_subject (第 138 行)
位置: db_load_subjects (第 125 行)
位置: db_reload_database (第 74 行)
位置: panel_protocols>ReloadNode (第 720 行)
位置: panel_protocols (第 46 行)
位置: tree_callbacks>@(h,ev)panel_protocols('ReloadNode',bstNodes(1)) (第 2723 行)
警告: Cannot open anatomy file
'G:\brainstorm_db\Test_001\anat\04liushuhan\subjectimage_postCT_spm_reslice_masked_spm_volct.mat'.
位置：db_parse_subject/io_getAnatomyInfo (第 273 行)
位置: db_parse_subject (第 157 行)
位置: db_parse_subject (第 138 行)
位置: db_load_subjects (第 125 行)
位置: db_reload_database (第 74 行)
位置: panel_protocols>ReloadNode (第 720 行)
位置: panel_protocols (第 46 行)
位置: tree_callbacks>@(h,ev)panel_protocols('ReloadNode',bstNodes(1)) (第 2723 行)
警告: Cannot open anatomy file 'G:\brainstorm_db\Test_001\anat\05liuyinglu_2016ft\subjectimage_anatomy3_volatlas.mat'.
位置：db_parse_subject/io_getAnatomyInfo (第 273 行)
位置: db_parse_subject (第 157 行)
位置: db_parse_subject (第 138 行)
位置: db_load_subjects (第 125 行)
位置: db_reload_database (第 74 行)
位置: panel_protocols>ReloadNode (第 720 行)
位置: panel_protocols (第 46 行)
位置: tree_callbacks>@(h,ev)panel_protocols('ReloadNode',bstNodes(1)) (第 2723 行)
警告: Cannot open anatomy file 'G:\brainstorm_db\Test_001\anat\05liuyinglu_2016ft\subjectimage_cobra_volatlas.mat'.
位置：db_parse_subject/io_getAnatomyInfo (第 273 行)
位置: db_parse_subject (第 157 行)
位置: db_parse_subject (第 138 行)
位置: db_load_subjects (第 125 行)
位置: db_reload_database (第 74 行)
位置: panel_protocols>ReloadNode (第 720 行)
位置: panel_protocols (第 46 行)
位置: tree_callbacks>@(h,ev)panel_protocols('ReloadNode',bstNodes(1)) (第 2723 行)
警告: Cannot open anatomy file 'G:\brainstorm_db\Test_001\anat\05liuyinglu_2016ft\subjectimage_hammers_volatlas.mat'.
位置：db_parse_subject/io_getAnatomyInfo (第 273 行)
位置: db_parse_subject (第 157 行)
位置: db_parse_subject (第 138 行)
位置: db_load_subjects (第 125 行)
位置: db_reload_database (第 74 行)
位置: panel_protocols>ReloadNode (第 720 行)
位置: panel_protocols (第 46 行)
位置: tree_callbacks>@(h,ev)panel_protocols('ReloadNode',bstNodes(1)) (第 2723 行)
警告: Cannot open anatomy file
'G:\brainstorm_db\Test_001\anat\05liuyinglu_2016ft\subjectimage_julichbrain_volatlas.mat'.
位置：db_parse_subject/io_getAnatomyInfo (第 273 行)
位置: db_parse_subject (第 157 行)
位置: db_parse_subject (第 138 行)
位置: db_load_subjects (第 125 行)
位置: db_reload_database (第 74 行)
位置: panel_protocols>ReloadNode (第 720 行)
位置: panel_protocols (第 46 行)
位置: tree_callbacks>@(h,ev)panel_protocols('ReloadNode',bstNodes(1)) (第 2723 行)
警告: Cannot open anatomy file 'G:\brainstorm_db\Test_001\anat\05liuyinglu_2016ft\subjectimage_lpba40_volatlas.mat'.
位置：db_parse_subject/io_getAnatomyInfo (第 273 行)
位置: db_parse_subject (第 157 行)
位置: db_parse_subject (第 138 行)
位置: db_load_subjects (第 125 行)
位置: db_reload_database (第 74 行)
位置: panel_protocols>ReloadNode (第 720 行)
位置: panel_protocols (第 46 行)
位置: tree_callbacks>@(h,ev)panel_protocols('ReloadNode',bstNodes(1)) (第 2723 行)
警告: Cannot open anatomy file 'G:\brainstorm_db\Test_001\anat\05liuyinglu_2016ft\subjectimage_mori_volatlas.mat'.
位置：db_parse_subject/io_getAnatomyInfo (第 273 行)
位置: db_parse_subject (第 157 行)
位置: db_parse_subject (第 138 行)
位置: db_load_subjects (第 125 行)
位置: db_reload_database (第 74 行)
位置: panel_protocols>ReloadNode (第 720 行)
位置: panel_protocols (第 46 行)
位置: tree_callbacks>@(h,ev)panel_protocols('ReloadNode',bstNodes(1)) (第 2723 行)
警告: Cannot open anatomy file 'G:\brainstorm_db\Test_001\anat\05liuyinglu_2016ft\subjectimage_thalamus_volatlas.mat'.
位置：db_parse_subject/io_getAnatomyInfo (第 273 行)
位置: db_parse_subject (第 157 行)
位置: db_parse_subject (第 138 行)
位置: db_load_subjects (第 125 行)
位置: db_reload_database (第 74 行)
位置: panel_protocols>ReloadNode (第 720 行)
位置: panel_protocols (第 46 行)
位置: tree_callbacks>@(h,ev)panel_protocols('ReloadNode',bstNodes(1)) (第 2723 行)
警告: Cannot open anatomy file
'G:\brainstorm_db\Test_001\anat\05liuyinglu_2016ft\subjectimage_tissues_cat12_volatlas.mat'.
位置：db_parse_subject/io_getAnatomyInfo (第 273 行)
位置: db_parse_subject (第 157 行)
位置: db_parse_subject (第 138 行)
位置: db_load_subjects (第 125 行)
位置: db_reload_database (第 74 行)
位置: panel_protocols>ReloadNode (第 720 行)
位置: panel_protocols (第 46 行)
位置: tree_callbacks>@(h,ev)panel_protocols('ReloadNode',bstNodes(1)) (第 2723 行)
警告: Cannot open anatomy file
'G:\brainstorm_db\Test_001\anat\10wujiyuan_2022tt\subjectimage_postCT_spm_reslice_masked_spm_volct.mat'.
位置：db_parse_subject/io_getAnatomyInfo (第 273 行)
位置: db_parse_subject (第 157 行)
位置: db_parse_subject (第 138 行)
位置: db_load_subjects (第 125 行)
位置: db_reload_database (第 74 行)
位置: panel_protocols>ReloadNode (第 720 行)
位置: panel_protocols (第 46 行)
位置: tree_callbacks>@(h,ev)panel_protocols('ReloadNode',bstNodes(1)) (第 2723 行)
警告: Cannot open anatomy file
'G:\brainstorm_db\Test_001\anat\21hujingran_2021tt\subjectimage_postCT_spm_reslice_masked_spm_volct.mat'.
位置：db_parse_subject/io_getAnatomyInfo (第 273 行)
位置: db_parse_subject (第 157 行)
位置: db_parse_subject (第 138 行)
位置: db_load_subjects (第 125 行)
位置: db_reload_database (第 74 行)
位置: panel_protocols>ReloadNode (第 720 行)
位置: panel_protocols (第 46 行)
位置: tree_callbacks>@(h,ev)panel_protocols('ReloadNode',bstNodes(1)) (第 2723 行)
警告: Cannot open anatomy file
'G:\brainstorm_db\Test_001\anat\24muxueting_2023tt\subjectimage_muxuetin_2023tt_postseeg_spm_reslice_masked_spm_volct.mat'.
位置：db_parse_subject/io_getAnatomyInfo (第 273 行)
位置: db_parse_subject (第 157 行)
位置: db_parse_subject (第 138 行)
位置: db_load_subjects (第 125 行)
位置: db_reload_database (第 74 行)
位置: panel_protocols>ReloadNode (第 720 行)
位置: panel_protocols (第 46 行)
位置: tree_callbacks>@(h,ev)panel_protocols('ReloadNode',bstNodes(1)) (第 2723 行)
警告: Cannot open anatomy file 'G:\brainstorm_db\Test_001\anat\25liuxingnan_2023tt\subjectimage_anat.mat'.
位置：db_parse_subject/io_getAnatomyInfo (第 273 行)
位置: db_parse_subject (第 157 行)
位置: db_parse_subject (第 138 行)
位置: db_load_subjects (第 125 行)
位置: db_reload_database (第 74 行)
位置: panel_protocols>ReloadNode (第 720 行)
位置: panel_protocols (第 46 行)
位置: tree_callbacks>@(h,ev)panel_protocols('ReloadNode',bstNodes(1)) (第 2723 行)
警告: Cannot open anatomy file
'G:\brainstorm_db\Test_001\anat\25liuxingnan_2023tt\subjectimage_tissues_segment_volatlas_02.mat'.
位置：db_parse_subject/io_getAnatomyInfo (第 273 行)
位置: db_parse_subject (第 157 行)
位置: db_parse_subject (第 138 行)
位置: db_load_subjects (第 125 行)
位置: db_reload_database (第 74 行)
位置: panel_protocols>ReloadNode (第 720 行)
位置: panel_protocols (第 46 行)
位置: tree_callbacks>@(h,ev)panel_protocols('ReloadNode',bstNodes(1)) (第 2723 行)
警告: Cannot open file
'G:\brainstorm_db\Test_001\data\000yanghanjie_2021ft\Epileptogenicity_volume\brainstormstudy.mat' : ignoring study
位置：db_parse_study (第 79 行)
位置: db_parse_study (第 174 行)
位置: db_parse_study (第 174 行)
位置: db_load_studies (第 141 行)
位置: db_reload_database (第 77 行)
位置: panel_protocols>ReloadNode (第 720 行)
位置: panel_protocols (第 46 行)
位置: tree_callbacks>@(h,ev)panel_protocols('ReloadNode',bstNodes(1)) (第 2723 行)
警告: Cannot open file
'G:\brainstorm_db\Test_001\data\000yanghanjie_2021ft\Epileptogenicity_volume_02\brainstormstudy.mat' : ignoring study
位置：db_parse_study (第 79 行)
位置: db_parse_study (第 174 行)
位置: db_parse_study (第 174 行)
位置: db_load_studies (第 141 行)
位置: db_reload_database (第 77 行)
位置: panel_protocols>ReloadNode (第 720 行)
位置: panel_protocols (第 46 行)
位置: tree_callbacks>@(h,ev)panel_protocols('ReloadNode',bstNodes(1)) (第 2723 行)
警告: Cannot open file 'G:\brainstorm_db\Test_001\data\08sunheze_2015ft\Epileptogenicity_volume\brainstormstudy.mat' :
ignoring study
位置：db_parse_study (第 79 行)
位置: db_parse_study (第 174 行)
位置: db_parse_study (第 174 行)
位置: db_load_studies (第 141 行)
位置: db_reload_database (第 77 行)
位置: panel_protocols>ReloadNode (第 720 行)
位置: panel_protocols (第 46 行)
位置: tree_callbacks>@(h,ev)panel_protocols('ReloadNode',bstNodes(1)) (第 2723 行)

Renoald · December 6, 2025, 6:59am

It looks like my Protocol got corrupted after I ran SPM12 in the same MATLAB session where Brainstorm was open.
If there are steps to rebuild the database/index, or a recommended recovery workflow, I’d greatly appreciate guidance.

Thanks in advance!

Renoald · December 6, 2025, 8:01am

Hi Brainstorm team,

After opening my protocol, clicking any data node triggers an error:

Error in gui_layout.m
Line 699: Index exceeds number of array elements. Index must not exceed 0.

Call stack:
> gui_layout.m>PositionFigure at 699
> gui_layout.m>TileWindows    at 597
> gui_layout.m>Update         at 50
> gui_layout.m at 33
> bst_figures.m>CreateFigure  at 232
> bst_figures.m at 59
> view_timeseries.m at 149
> tree_callbacks.m at 274
> bst_call.m at 28
> panel_protocols.m>CreatePanel/protocolTreeClicked_Callback at 125
> bst_call.m at 28
> panel_protocols.m>@(h,ev)bst_call(@protocolTreeClicked_Callback,h,ev) at 75

This now happens for every file I click. The data are very important to me—any advice on how to repair or recover would be greatly appreciated.

Environment: Brainstorm [version/build], MATLAB [version/update], OS [Windows/macOS/Linux].
(Notes: my MATLAB UI is in Simplified Chinese; the message reads “索引超过元素组的数量，索引不能超过 0”.)

Thank you so much!

Best regards,

Raymundo.Cassani · December 8, 2025, 2:23pm

The issue seems to be related to the position of the figures in your screen(s).

Try changing the Window layout options to None

Please provide the following information, so we can better assist you:

Brainstorm version
Matlab version
Java version
OS and version
Number of screens and their configuration (mirror, horizontal extended, vertical extended, other)

You can find the first four points in the main Brainstorm window, in the menu Help > System info

Renoald · February 2, 2026, 9:19am

Dear Brainstorm team,

Apologies for the long delay in my response. The previous issue I posted about has been resolved. However, my main problem now is related to restoring a BIDS-formatted database.

The Scenario:

I moved my database (BIDS format) to a new location.
To force a database refresh, I deleted protocol.mat and the brainstormstudy.mat files within the subject folders, expecting Reload to rebuild the index.

The Current Issue: After reloading the protocol:

Brainstorm correctly identifies the subjects and links to the Raw files.
However, it fails to register the imported epochs (data_*.mat) and channel files (channel.mat) that already exist in the folders.
The protocol tree only shows the link to the raw file.

My Observations:

I inspected the newly generated brainstormstudy.mat. It appears to be reset/empty and lacks the Data structure array that indexes the processed .mat files.
The data_*.mat and channel.mat files are physically present on the disk but are now "orphaned" (not visible in the GUI).
Since this is a BIDS structure (deep folder hierarchy), I suspect the standard Reload is skipping these non-raw files.

My Question: Is there a script or command to force-scan and re-register these existing data_*.mat files back into the database index? I want to avoid re-importing everything from the raw files.

Thank you for your time and help

Raymundo.Cassani · February 2, 2026, 2:26pm

Deleting protocol.mat is correct. But you should not delete the files brainstormstudy.mat, that makes them not visible when reloading the Protocol.

This suggest to me that the brainstormstudy.mat was not deleted for the raw Study folders. The ones with name starting with @raw....

That Data structure is not saved in the brainstormstudy.mat. That one is part of the protocol.mat. The file brainstormstudy.mat only contains a list of good/bad trials, date of Study and name of Study.

Because the brainstormstudy.mat file was deleted from those folders.
This file is not regenerated based on the data.

The directory for a Brainstorm Protocol and a BIDS directory has similarities, but the Protocol directory is not a BIDS structure. Reload is skipping the Study folders without a brainstormstudy.mat file.

In your original Brainstorm database. If you want to regenerate the protocol metadata that is stored as a Matlab structure in the protocol.mat file.

In Brainstorm, make sure that the Protocol is not loaded. If so, go to File > Delete protocol > Only detach from database
Close Brainstorm
Delete the protocol.mat file in the THAT_PROTOCOL/data directory
Start Brainstorm, and load the protocol: File > Load protocol > Load from folder

Renoald · February 2, 2026, 4:33pm

Dear Francois,

Thank you for your guidance. I followed the steps exactly (Detached the protocol, deleted protocol.mat in the data directory, and reloaded it using "Load from folder"). Unfortunately, it did not resolve the issue, and I am seeing some very strange behavior.

1. Error Logs: Upon reloading, the MATLAB command window is flooded with "Cannot open anatomy file" and "Cannot open file... brainstormstudy.mat" warnings for almost every subject (see the log below). It seems Brainstorm is physically unable to access or read the .mat files, even though they exist on the disk.

2. A Crucial Discovery: I noticed a very specific phenomenon:

Sort by Subject: The functional data is invisible.
Sort by Condition: The imported data (epochs) appears correctly!

This suggests the data files are recognized, but the link between the "Studies" and the "Subjects" is broken in the database metadata. Even when I try to re-import data from a raw link, the new entries only show up in the "Condition" view and remain hidden in the "Subject" view.

3. Anatomy Errors: Additionally, I get warnings like: Warning: Cannot open anatomy file '...\anat\01gaoyibo_2021ft\subjectimage_3DT1.mat'. These files are definitely there. Is it possible that moving the database between drives or a crash has caused some form of file permission issue or a corruption in the BIDS-style folder parsing?

I have attached the full error log. What would you suggest as the next step to re-establish the Subject-Study relationship?

I have uploaded my protocol.mat file and the data files from one of the affected subjects for your reference. By the way, my anatomy files are working perfectly fine without any issues.

Best regards,

>> brainstorm

BST> Starting Brainstorm:
BST> =================================
BST> Version: 26-Jan-2026
BST> Warning: Brainstorm is not fully tested and supported on the New Matlab Desktop.
BST> Compiling main interface files...
BST> Deleting old process reports...
BST> Loading configuration file...

BST> Checking internet connectivity... ok
BST> Update available online: 29-Jan-2026
BST> Initializing user interface...

BST> Starting OpenGL engine... hardware: ANGLE (NVIDIA, NVIDIA GeForce RTX 5060 (0x00002D05) Direct3D11 vs_5_0 ps_5_0, D3D11)
BST> Plugin spm12: D:\Toolbox\spm12_7219
BST> Reading process folder...

BST> Loading current protocol...

BST> =================================

BST> Brainstorm stopped.

>> brainstorm

BST> Starting Brainstorm:
BST> =================================
BST> Version: 26-Jan-2026
BST> Warning: Brainstorm is not fully tested and supported on the New Matlab Desktop.
BST> Compiling main interface files...
BST> Deleting old process reports...
BST> Loading configuration file...
BST> Checking internet connectivity... ok
BST> Update available online: 29-Jan-2026
BST> Initializing user interface...

BST> Starting OpenGL engine... hardware: ANGLE (NVIDIA, NVIDIA GeForce RTX 5060 (0x00002D05) Direct3D11 vs_5_0 ps_5_0, D3D11)
BST> Plugin spm12: D:\Toolbox\spm12_7219
BST> Reading process folder...

BST> Loading current protocol...

BST> =================================

Warning: Cannot open anatomy file 'D:\Database\brainstorm_db\Test_001\anat\01gaoyibo_2021ft\subjectimage_3DT1.mat'.
> 位置：[db_parse_subject/io_getAnatomyInfo](matlab:matlab.lang.internal.introspective.errorDocCallback('db_parse_subject/io_getAnatomyInfo', 'D:\Toolbox\brainstorm3\toolbox\db\private\db_parse_subject.m', 273)) ([第 273 行](matlab: opentoline('D:\Toolbox\brainstorm3\toolbox\db\private\db_parse_subject.m',273,0)))
位置: [db_parse_subject](matlab:matlab.lang.internal.introspective.errorDocCallback('db_parse_subject', 'D:\Toolbox\brainstorm3\toolbox\db\private\db_parse_subject.m', 157)) ([第 157 行](matlab: opentoline('D:\Toolbox\brainstorm3\toolbox\db\private\db_parse_subject.m',157,0)))

Raymundo.Cassani · February 3, 2026, 2:20am

The shared functional data for the subject 07sunbowen_ft can be loaded without troubles.
This is what I did:

Start Brainstorm
Create a new Protocol TEST_FORUM_DB
- No, use individual anatomy
- No, use one channel file per acquisition run
Create a new Subject called 07sunbowen_ft
Edit the subject to use:
- Yes, use default anatomy
Close Brainstorm
Delete the contents of the directory TEST_FORUM_DB/data/07sunbowen_ft
Paste the shared directories into TEST_FORUM_DB/data/07sunbowen_ft
Start Brainstorm
Right-click on the Protocol node, and select Reload

|

You can check that by trying to open the files in Matlab with the Matlab function load()

The error just suggest there is an issue opening the file with load()
Check the tests below

Renoald:

Warning: Cannot open anatomy file 'D:\Database\brainstorm_db\Test_001\anat\01gaoyibo_2021ft\subjectimage_3DT1.mat'.
> 位置：[db_parse_subject/io_getAnatomyInfo](matlab:matlab.lang.internal.introspective.errorDocCallback('db_parse_subject/io_getAnatomyInfo', 'D:\Toolbox\brainstorm3\toolbox\db\private\db_parse_subject.m', 273)) ([第 273 行](matlab: opentoline('D:\Toolbox\brainstorm3\toolbox\db\private\db_parse_subject.m',273,0)))
位置: [db_parse_subject](matlab:matlab.lang.internal.introspective.errorDocCallback('db_parse_subject', 'D:\Toolbox\brainstorm3\toolbox\db\private\db_parse_subject.m', 157)) ([第 157 行](matlab: opentoline('D:\Toolbox\brainstorm3\toolbox\db\private\db_parse_subject.m',157,0)))

Please check that:

This file exist in your HDD, and that this file exist

'D:\Database\brainstorm_db\Test_001\anat\01gaoyibo_2021ft\subjectimage_3DT1.mat'`

This file can be loaded in Matlab

load('D:\Database\brainstorm_db\Test_001\anat\01gaoyibo_2021ft\subjectimage_3DT1.mat')

It is possible to load the Comment variable from that file

load('D:\Database\brainstorm_db\Test_001\anat\01gaoyibo_2021ft\subjectimage_3DT1.mat', 'Comment')

P.S. Are you sure the the database lives in the drive D:\?

Renoald · February 3, 2026, 4:49am

It is truly strange that the files work perfectly on your end while my system keeps throwing "Cannot open file" warnings. Here is an update on my investigation:

1. Potential Cause: SPM12 Conflict I realized that these issues began after I mistakenly ran SPM12 registration manually within the same Matlab instance where Brainstorm was running. This might have caused a conflict or corrupted how Brainstorm handles the file pointers.

2. Damaged Anatomy & Residual Info: I found that the anatomy file for one specific subject is indeed corrupted: D:\Database\brainstorm_db\Test_001\anat\01gaoyibo_2021ft\subjectimage_3DT1.mat

Even though I have manually deleted both the anatomy and data files for this subject from the hard drive, Brainstorm seems to retain "ghost" information of this subject in the database. Every time I reload, it still tries to access these non-existent files and triggers the warnings.

3. Current Status: My database tree still looks like this (attached image), where imported data is missing in "Functional data (sort by subjects)" but exists in "Sort by conditions."

Since you can open my protocol.mat without issues, could this be a local cache problem (e.g., in brainstorm.mat config file) or a permission issue triggered by the SPM12 crash? How can I completely "purge" these residual subject entries so I can start fresh for those specific folders?

Best regards,

Raymundo.Cassani · February 3, 2026, 2:09pm

Please open the file manually with the function load() so you can verify if the .m files in question are valid Matlab files.

This could be the case IFF you explicitly modify the files in the Brainstorm database.
Otherwise, SPM12 does not modify the Brainstorm database

Please check as indicated in the previous post.
Firstly, check if the .mat file is a valid Matlab file.

Please read carefully my previous post. I did not "open the protocol.mat" I just tested in the shared functional files organized as part of a valid Brainstorm database, and they are.

I'm not sure what do you mean with " permission issue triggered by the SPM12 crash?".
Again, please try to open the files in Matlab without starting Brainstorm, to check the access and integrity of the files.

To reset Brainstorm you can use the option Reset database in File > Edit preferences, this option will:

Detach all the protocols from the database (without deleting any file)
Reset all the Brainstorm and processes preferences
Restart Brainstorm as if it was the first time on the computer

Best,
Raymundo

Renoald · February 3, 2026, 4:10pm

Thank you very much for your continued patience and help. It truly means a lot to me.

Upon further inspection, you are correct: many .mat files in the anat directory are indeed corrupted. I cannot manually load those specific .mat files in Matlab either.

This corruption likely occurred during a previous incident where I accidentally deleted the database and then attempted to recover the data. What's confusing is that my Functional data (sort by subject) was displaying normally for a while after that recovery, but then suddenly failed recently for unknown reasons.

My question now is: Is there a way to force Brainstorm to display the functional data correctly again? For example, if I re-import the anatomy data for these subjects, will Brainstorm be able to re-link the existing data_*.mat files to the new subject structures?

I am trying to find a way to save the processed SEEG data without having to re-process everything from the raw recordings.

Best regards,