Scripting Exported Scouts Error

Discussions
1

Hello Brainstorm Team,

I am trying extract the scout time series in MATLAB in order to run coherence. I have a lot of subjects (178) so I need to automate this process. In trying to automate this I have noticed I can either run extract scout time series and proceed to coherence brainstorm script or I can apply the scouts in the coherence script. However, whenever I do either the atlas I have chosen is not transferred over.

In my code I am pulling in the correct file (the same mat file that I pull down in the gui) as the sfile:

sFiles = wfu_find_files('data_0raw',session_dir);
sFiles = char(sFiles);
% Start a new report
bst_report('Start', sFiles);

Next I run this code:

% Process: Scouts time series: [68 scouts]
sFiles = bst_process('CallProcess', 'process_extract_scout', sFiles, [], ...
'timewindow', [0, 4], ...
'scouts', {'Desikan-Killiany', {'bankssts L', 'bankssts R', 'caudalanteriorcingulate L', 'caudalanteriorcingulate R', 'caudalmiddlefrontal L', 'caudalmiddlefrontal R', 'cuneus L', 'cuneus R', 'entorhinal L', 'entorhinal R', 'frontalpole L', 'frontalpole R', 'fusiform L', 'fusiform R', 'inferiorparietal L', 'inferiorparietal R', 'inferiortemporal L', 'inferiortemporal R', 'insula L', 'insula R', 'isthmuscingulate L', 'isthmuscingulate R', 'lateraloccipital L', 'lateraloccipital R', 'lateralorbitofrontal L', 'lateralorbitofrontal R', 'lingual L', 'lingual R', 'medialorbitofrontal L', 'medialorbitofrontal R', 'middletemporal L', 'middletemporal R', 'paracentral L', 'paracentral R', 'parahippocampal L', 'parahippocampal R', 'parsopercularis L', 'parsopercularis R', 'parsorbitalis L', 'parsorbitalis R', 'parstriangularis L', 'parstriangularis R', 'pericalcarine L', 'pericalcarine R', 'postcentral L', 'postcentral R', 'posteriorcingulate L', 'posteriorcingulate R', 'precentral L', 'precentral R', 'precuneus L', 'precuneus R', 'rostralanteriorcingulate L', 'rostralanteriorcingulate R', 'rostralmiddlefrontal L', 'rostralmiddlefrontal R', 'superiorfrontal L', 'superiorfrontal R', 'superiorparietal L', 'superiorparietal R', 'superiortemporal L', 'superiortemporal R', 'supramarginal L', 'supramarginal R', 'temporalpole L', 'temporalpole R', 'transversetemporal L', 'transversetemporal R'}}, ...
'scoutfunc', 3, ... % PCA
'isflip', 1, ...
'isnorm', 0, ...
'concatenate', 0, ...
'save', 1, ...
'addrowcomment', 1, ...
'addfilecomment', 1);

This results in the sFiles being cleared out entirely from the MATLAB workspace.

After looking closer at the issue in the bst_process.m file line 2130 results in answers =1 but in line 2131 the defVal is .

I can only post one picture so here is what everything looks like during the for loop in the bst_process after running the first i which is "timewindow"...

image
image1471×844 77.9 KB

Could you please help me with this issue I am running into ?

2

That's correct. You could compute coherence (and other connectivity metrics) at the scout level directly.
There is no need to extract the scout time series, and then compute coherence.

It seems your function here returns the raw data files these are the recordings, not the sources files, this is the reason why the process_extract_scout fails after this.

You need to find the sources (or links) related to those raw data files.

% First get the path for the raw file
% I believe your function 'wfu_find_files()' does that
% For example:
fileRaw = 'Subject01/@rawCondition/data_0raw_Condition.mat'

% Get all Sources related to such raw file
[sStudy, iStudy, iResults] = bst_get('ResultsForDataFile', fileRaw);
fileSources = {sStudy.Result(iResults).FileName};

% Then you can use the process to extract scout

This is because the process fails, see the comment above.

If you want to automate your pipeline, we suggest you to perform it once on the GUI. Then it is possible to create a script performs the same that was instructed in the Pipeline editor. See:
https://neuroimage.usc.edu/brainstorm/Tutorials/Scripting#Starting_a_new_script