[Eeglablist] FW: script to batch process multiple Neuroscan CNT files

[Jeffrey Eriksen]

Cedric and Ben,

I combined your suggestions and it worked well. Here is my final version. I know it could be shortened, but I was using the extra lines for troubleshooting. The nesting was actually 4-deep: phase, subject, session, and run, with some variability inn numbers of sub-folders at each lever, so the "files = dir('**/*.cnt')" really helped out. I can keep the organization and do all the processing in-place.

Thanks so much. I will be able to modify this to rename the SET files to my liking, and add further processing steps.

Cheers!

-Jeff

dataFolder = ['D:\Sorg memory project\Budata'];
cd(dataFolder)
files = dir('**/*.cnt');
nSessions = size(files,1);
filenames = {files.name};
filepaths = {files.folder};
eeglab; close;

for iSession = 1:nSessions
    path = filepaths{iSession};
    file = filenames{iSession};
    pathfile= strcat(path, '\', file);
    cd(path)
    EEG = pop_loadcnt(pathfile, 'dataformat', 'auto', 'memmapfile', '');
    EEG = pop_saveset(EEG,'filename',[file(1:end-4) '.set'],'filepath',path);
end

disp('Done!')

-----Original Message-----
From: Cedric Cannard <ccannard at protonmail.com> 
Sent: Tuesday, March 14, 2023 11:17 AM
To: Jeffrey Eriksen <jeriksen at downeurobiology.org>
Cc: eeglablist at sccn.ucsd.edu
Subject: RE: [Eeglablist] FW: script to batch process multiple Neuroscan CNT files

Hi Jeff,

There was a typo (missing parenthesis to close fullfile call). 

You need to edit with something like this for going into subfolders. Edit number of sessions and runs below:

dataFolder = 'D:\Sorg memory project\BU data\cue_reactivity_1'; nSessions = 3;  % edit with your number of sessions here
nRuns = 3;      % edit with your number of runs here

eeglab; close;
for iSession = 1:nSessions
    session = sprintf('s%2.2d', iSession);
    for iRun = 1:nRuns
        run = sprintf('run%g', iRun);
        filepath = fullfile(dataFolder, session, run);
        cd(filepath)
        fileNames = dir('*.cnt');
        fileNames = {fileNames.name};

        for iFile = 1:length(fileNames)
            filename = fileNames{iFile};
            EEG = pop_loadcnt(fullfile(filepath, filename), 'dataformat', 'auto', 'memmapfile', '');
            EEG = pop_saveset(EEG,'filename',[filename(1:end-5) '.set'],'filepath',filepath);
        end
    end
end

And check out the pipelines Arno sent ;)

Cedric



------- Original Message -------
On Tuesday, March 14th, 2023 at 9:48 AM, Jeffrey Eriksen <jeriksen at downeurobiology.org> wrote:


> Hi
> 
> Cedric
> 
> 
> ,
> 
> Thank you for writing out a whole script for me. If it is not too much to ask, can you modify it to scan all subfolders? I was perhaps not totally clear in my initial request. The CNT files are nested in several layers by subject and run.
> 
> More importantly, I encountered an error in the call to loadcnt. I do not presume that you know the inner workings of loadcnt, but could you take a look at the error message and see if it is something you could figure out? In the meantime I will look to see who wrote it and consider writing them directly.
> 
> -Jeff
> 
> My version (for a particular subject and run):
> % scan for and convert CNT files to SET files
> 
> dataFolder = 'D:\Sorg memory project\BU 
> data\cue_reactivity_1\s03\run1';
> cd(dataFolder)
> filenames = dir('*.cnt');
> filenames = {filenames.name};
> eeglab; close;
> 
> for iFile = 1:length(filenames)
> filename = filenames{iFile};
> EEG = pop_loadcnt(fullfile(dataFolder, filename, 'dataformat', 'auto', 
> 'memmapfile', '')); EEG = 
> pop_saveset(EEG,'filename',[filename(1:end-5) 
> '.set'],'filepath',dataFolder); end
> disp('Done!')
> 
> output to command line:
> 
> > > scan_convert
> 
> eeglab: options file is C:\Users\Jeff\eeg_options.m Retrieving plugin 
> versions from server...
> Retrieving download statistics...
> EEGLAB: adding "Biosig" v3.8.1 to the path
> EEGLAB: adding "Cleanline" v2.00 (see >> help eegplugin_cleanline)
> 
> EEGLAB: adding "Fileio" v20230309 to the path
> EEGLAB: adding "ICLabel" v1.4 (see >> help eegplugin_iclabel)
> 
> EEGLAB: adding "MFFMatlabIO" v4.1 (see >> help eegplugin_mffmatlabio)
> 
> EEGLAB: adding "MFFimport" v2.3 (see >> help eegplugin_mffimport)
> 
> EEGLAB: adding "clean_rawdata" v2.8 (see >> help 
> eegplugin_clean_rawdata)
> 
> EEGLAB: adding "dipfit" v5.0 (see >> help eegplugin_dipfit)
> 
> EEGLAB: adding "egilegacy" v1.0 (see >> help eegplugin_egilegacy)
> 
> EEGLAB: adding "firfilt" v2.7.1 (see >> help eegplugin_firfilt)
> 
> EEGLAB: adding "neuroscanio" v1.6 (see >> help eegplugin_neuroscanio)
> 
> You are using the latest version of EEGLAB.
> 9 for iFile = 1:length(filenames)
> Error using fread
> Invalid file identifier. Use fopen to generate a valid file identifier.
> 
> Error in loadcnt (line 110)
> h.rev = fread(fid,12,'char');
> 
> Error in pop_loadcnt (line 132)
> r = loadcnt( fullFileName);
> 
> Error in scan_convert (line 11)
> EEG = pop_loadcnt(fullfile(dataFolder, filename, 'dataformat', 'auto', 
> 'memmapfile', ''));
> 
> 
> 
> -----Original Message-----
> From: Cedric Cannard ccannard at protonmail.com
> 
> Sent: Sunday, March 12, 2023 12:13 PM
> To: Jeffrey Eriksen jeriksen at downeurobiology.org
> 
> Cc: eeglablist at sccn.ucsd.edu
> Subject: Re: [Eeglablist] FW: script to batch process multiple 
> Neuroscan CNT files
> 
> Hi Jeff,
> 
> After installing the Neuroscanio plugin, this should do:
> 
> dataFolder = 'pathToYourDataFolder';
> cd(dataFolder )
> filenames = dir('*.cnt');
> filenames = {filenames.name};
> eeglab; close;
> 
> for iFile = 1:length(filenames)
> filename = filenames{iFile};
> EEG = pop_loadcnt(fullfile(dataFolder, filename, 'dataformat', 'auto', 
> 'memmapfile', '');
> 
> EEG = pop_saveset(EEG,'filename',[filename(1:end-5) 
> '.set'],'filepath',dataFolder);
> 
> end
> disp('Done!')
> 
> 
> Cedric
> 
> 
> 
> ------- Original Message -------
> On Friday, March 10th, 2023 at 10:04 AM, Jeffrey Eriksen jeriksen at downeurobiology.org wrote:
> 
> 
> 
> > Hello,
> > 
> > I have 327 Neuroscan CNT files. Does anyone know of a script that I could use or modify to do the following:
> > 
> > 1. Scan a set of folders and find all the CNT files 2. Import them 
> > using the neuroscanio plugin 3. Save them as SET format
> > 
> > Thanks,
> > -Jeff Eriksen
> > 
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