[Eeglablist] script to batch process multiple Neuroscan CNT files

[Arnaud Delorme]

Hi Jeff,

Below is the list of all EEGLAB pipelines.

https://urldefense.com/v3/__https://eeglab.org/tutorials/11_Scripting/automated_pipeline.html__;!!Mih3wA!BQP5CBrLMHrrvZTkzZLJrYKN2hAWtuPrvO8S2W_-edj8lwePYHkgxCJTHBn91vMnDAyOwmGBNxwbgYGuv3oJ1t-R$ 

Cheers,

Arno

> On Mar 14, 2023, at 6:48 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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