Export source estimation roi data with bug

hasibagen · January 5, 2022, 8:34am

I'm trying to export my traceability results based on the roi I made, but this error window pops up and I need to click confirm manually.
The cortical file associated with these sources no longer exists. Please use: s001_tess_cortex.mat.

I would like to ask if there is any solution for this?
Q1: I first want to ask if it is possible to generate source results with cortex files after preprocessing, or roi exported data with cortex files?
Because I have more than 100 subjects, each subject has 12 evoke files preprocessed in MNE and imported into brainstorm.
My subjects are eeg data of different children from 7-18 years old. So I calculated the brain templates and open meeg bem head models for children aged 7-18 years in advance, and then copied the brain templates and bem models for each subject of the corresponding age. If the bem is regenerated for each subject, there is no such problem. But I have more than 100 subjects, and it takes too long to regenerate bem for each subject.

2 Is there a code to fix this popup or blank cortex file? The one in the previous forum doesn't seem to work.

Thank you very much for your help!
Looking forward to your reply!

Appendix 1:

I have found people with the same problem in the forum

But it keeps reporting errors when following this code to make changes.

[sMat, matName] = in_bst(sFiles{i});
ProtocolInfo = bst_get('ProtocolInfo');
sMat.SurfaceFile = 'SubjectName/cortexfile.mat'; % modify this line
outputFile = bst_fullfile(ProtocolInfo.STUDIES, sFiles{i})
bst_save(outputFile, sMat, 'v6').

It seems that the person who asked this question didn't succeed in using this code, and ended up using AutoHotKey to solve the problem. But I'm using ubuntu and can't use this solution.

This is my code.

Subj={ 
    's001',
};
for i=1:length(Subj) 
% Input files
sFiles = [];
SubjectNames = {Subj{i}};
RawFiles = {...
strcat( '/home/jade/data/loopvis/nh_evoke/',Subj{i}, 'evokev1-epo.fif'), ...
strcat( '/home/jade/data/loopvis/nh_evoke/',Subj{i}, 'evokev2-epo.fif'), ...
strcat( '/home/jade/data/loopvis/nh_evoke/',Subj{i}, 'evokev3-epo.fif'), ...
strcat( '/home/jade/data/loopvis/nh_evoke/',Subj{i}, 'evokev4-epo.fif'), };

% Start a new report
bst_report('Start', sFiles);

% Processing. Import MEG/EEG: existing ephemeral data
sFiles = bst_process('CallProcess', 'process_import_data_epoch', sFiles, [], ...
    'subjectname', SubjectNames{1}, ...
    'condition', '', ...
    'dataFiles', {{RawFiles{1}; RawFiles{2}; RawFiles{3}; RawFiles{4}}, 'FIF'}, ...
    'iepochs', [], ...
    'eventtypes', '', ...
    'createcond', 0, ...
    'channelalign', 0, ...
    'usectfcomp', 0, ...
    'usessp', 0, ...
    'freq', [], ...
    'baseline', []).


[sMat, matName] = in_bst(sFiles);
ProtocolInfo = bst_get('ProtocolInfo');
sMat.SurfaceFile = 'n001/cortexfile.mat'; % change this line
outputFile = bst_fullfile(ProtocolInfo.STUDIES, sFiles{i})
bst_save(outputFile, sMat, 'v6').

% Save and display the report
ReportFile = bst_report('Save', sFiles);
bst_report('Open', ReportFile);
% bst_report('Export', ReportFile, ExportDir);
End

This one is reporting an error

 [sMat, matName] = in_bst(sFiles);
The output parameter "sMatrix" (and possibly other parameters) is not assigned when calling "in_bst".

outputFile = bst_fullfile(ProtocolInfo.STUDIES, sFiles{i})
Brace indexing is not supported for this type of variable.

Appendix 2:
This is all my processing scripts

Subj={    's001',
};

for i=1:length(Subj)

% Input files
sFiles = [];
SubjectNames = {Subj{i}};
RawFiles =  {...
strcat( '/home/jade/data/loopvis/ci_evoke/',Subj{i},'evokev1-epo.fif'), ...
strcat( '/home/jade/data/loopvis/ci_evoke/',Subj{i},'evokev2-epo.fif'), ...
strcat( '/home/jade/data/loopvis/ci_evoke/',Subj{i},'evokev3-epo.fif'), ...
strcat( '/home/jade/data/loopvis/ci_evoke/',Subj{i},'evokev4-epo.fif'), };

% Start a new report
bst_report('Start', sFiles);

% Process: Import MEG/EEG: Existing epochs
sFiles = bst_process('CallProcess', 'process_import_data_epoch', sFiles, [], ...
    'subjectname',  SubjectNames{1}, ...
    'condition',    '', ...
    'datafile',     {{RawFiles{1}; RawFiles{2}; RawFiles{3}; RawFiles{4}}, 'FIF'}, ...
    'iepochs',      [], ...
    'eventtypes',   '', ...
    'createcond',   0, ...
    'channelalign', 0, ...
    'usectfcomp',   0, ...
    'usessp',       0, ...
    'freq',         [], ...
    'baseline',     []);

% Process: Set channel file
sFiles = bst_process('CallProcess', 'process_import_channel', sFiles, [], ...
    'channelfile',  {RawFiles{1}; RawFiles{2}; RawFiles{3}; RawFiles{4}}, ...
    'usedefault',   114, ...  % NotAligned: GSN HydroCel 128 E1
    'channelalign', 1, ...
    'fixunits',     1, ...
    'vox2ras',      1);

% Process: Set channels type
sFiles = bst_process('CallProcess', 'process_channel_settype', sFiles, [], ...
    'sensortypes', 'E8,E14,E21,E25,E125,E126,E127,E128', ...
    'newtype',     'EOG');

% Process: Average: By trial group (folder average)
sFiles = bst_process('CallProcess', 'process_average', sFiles, [], ...
    'avgtype',       5, ...  % By trial group (folder average)
    'avg_func',      1, ...  % Arithmetic average:  mean(x)
    'weighted',      0, ...
    'keepevents',    0);

% Process: Compute covariance (noise or data)
sFiles = bst_process('CallProcess', 'process_noisecov', sFiles, [], ...
    'baseline',       [-0.1, 0], ...
    'datatimewindow', [0, 0.5], ...
    'sensortypes',    'EEG', ...
    'target',         1, ...  % Noise covariance     (covariance over baseline time window)
    'dcoffset',       1, ...  % Block by block, to avoid effects of slow shifts in data
    'identity',       0, ...
    'copycond',       0, ...
    'copysubj',       0, ...
    'copymatch',      0, ...
    'replacefile',    3, ...  % Keep
    'source_abs',     0);

% Process: Compute sources [2018]
sFiles = bst_process('CallProcess', 'process_inverse_2018', sFiles, [], ...
    'output',  2, ...  % Kernel only: one per file
    'inverse', struct(...
         'Comment',        'sLORETA: EEG', ...
         'InverseMethod',  'minnorm', ...
         'InverseMeasure', 'sloreta', ...
         'SourceOrient',   {{'fixed'}}, ...
         'Loose',          0.2, ...
         'UseDepth',       0, ...
         'WeightExp',      0.5, ...
         'WeightLimit',    10, ...
         'NoiseMethod',    'reg', ...
         'NoiseReg',       0.1, ...
         'SnrMethod',      'fixed', ...
         'SnrRms',         1e-06, ...
         'SnrFixed',       3, ...
         'ComputeKernel',  1, ...
         'DataTypes',      {{'EEG'}}));

% Save and display report
ReportFile = bst_report('Save', sFiles);
bst_report('Open', ReportFile);
% bst_report('Export', ReportFile, ExportDir);
end

% Script generated by Brainstorm (28-Dec-2021)
% Input files
sFiles = {...
   'link|s001/s001evokev1-epo/results_sLORETA_EEG_KERNEL_220105_0928.mat|s001/s001evokev1-epo/data_Epoch_average_220105_0916.mat'};

% Start a new report
bst_report('Start', sFiles);

% Process: Scouts time series: Cortex L Cortex R
sFiles = bst_process('CallProcess', 'process_extract_scout', sFiles, [], ...
    'timewindow',     [-0.1, 0.5], ...
    'scouts',         {'Structures', {'Cortex L', 'Cortex R'}}, ...
    'scoutfunc',      1, ...  % Mean
    'isflip',         1, ...
    'isnorm',         0, ...
    'concatenate',    1, ...
    'save',           1, ...
    'addrowcomment',  1, ...
    'addfilecomment', 1);

% Save and display report
ReportFile = bst_report('Save', sFiles);
bst_report('Open', ReportFile);

Francois · January 7, 2022, 4:54pm

The cortical file associated with these sources no longer exists. Please use: s001_tess_cortex.mat.
I would like to ask if there is any solution for this?

Not deleting or renaming the file...
When exactly is this message showing up?

I first want to ask if it is possible to generate source results with cortex files after preprocessing, or roi exported data with cortex files?

I'm not sure I understand your question. Can you please reformulate?

So I calculated the brain templates and open meeg bem head models for children aged 7-18 years in advance

Make sure you project the electrodes positions on the scalp for each age group.

If the bem is regenerated for each subject, there is no such problem. But I have more than 100 subjects, and it takes too long to regenerate bem for each subject.

If the electrodes positions and the anatomy files are strictly the same for all the subjects for one age template, you can safely copy-paste the OpenMEEG head model from your local template to each subject:

With the GUI: CTRL+C / CTRL+V from the Brainstorm database explorer
From a script: use function db_set_headmodel:
- brainstorm3/toolbox/db/db_set_headmodel.m at master · brainstorm-tools/brainstorm3 · GitHub
- https://neuroimage.usc.edu/brainstorm/Tutorials/Scripting?highlight=(db_reload)#Reference:_File_manipulation

I have found people with the same problem in the forum

I don't think the forum post you refer to is related to your problem.
The error message you report indicate that there is an issue with your database. You removed or renamed the surface that you previously used for some computation.
Fix your database, workflow or scripts in order not to change the name of the surface files.

This is my code.

I don't understand what you're trying to do with the piece of code you copy-pasted from the other forum post.

hasibagen · January 11, 2022, 11:18am

I have the fmri templates for ages 7-18, and the head models generated for each template, and all templates and electrode files for all subjects are uniform files.

Subject 1 uses the mri template and head model of an 8 year old child, then subject 2 also uses the mri template and head model of an 8 year old child, I copy the head model from subject 1 to subject 2 using the GUI: CTRL+C / CTRL+V from the Brainstorm database explorer.

Then I do the source estimation and export the source estimation result in the roi, Brainstorm will report an error in the gui window,

The cortical file associated with these sources no longer exists. Please use: s001_tess_cortex.mat.

I would like to ask how to solve this error.

Francois · January 12, 2022, 9:35am

Please use: s001_tess_cortex.mat.

If your file is really called s001_tess_cortex.mat, then you manipulated the contents of the database manually, you may have damaged something on the way. The file names generated by Brainstorm are all starting with the file type (eg. 'tess_...mat`). Please do not manipulate the files outside of the Brainstorm database explorer if you are not 100% sure of what you are doing. Or if you are decided to modify the file structures, please respect all the conventions.

Starting by reading the Scripting tutorial might help you:
https://neuroimage.usc.edu/brainstorm/Tutorials/Scripting

The cortical file associated with these sources no longer exists.

When copying the head model with the GUI, the field SurfaceFile should be emptied, exactly to avoid this error you reported.

Example, based on the EEG/Epilepsy tutorial:
I duplicated the subject, then deleted the head models in the copied subject, and finally copy the OpenMEEG headmodel into the new subject. I right-click > File > View file contents on the original file and the copy. You can see that the copied file as no SurfaceFile reference, and therefore no possibility of generating the error you reported.

Your problem resides somewhere else than in the copy of the head model.
If you can't figure out the problem, please reload your protocol, then make sure the error is still there, and post screen captures of your database explorer showing all the files involved in the computation: cortex file (with the mouse over the file to show the tooltip with the file name), channel file, head model before copy, head model after copy. Include screen captures of the file contents as well.