bidsCopyRawFolder function

[CerenB]

my not be working in matlab?
Basically it does not create a copy of sub-001 folder into derivatives folder.

[Remi-Gau]

does the script demo/batch_download_run.m work?

bidsCopyRawFolder(opt, 1); is at line 89 on that one. Make sure it is not commented out.

[CerenB]

Hmm, not really.

derivatives directory created: /Users/battal/Documents/GitHub/CPPLab/CPP_BIDS_SPM_pipeline/demo/output/MoAEpilot/../derivatives/SPM12_CPPL 
K>> fullfile(rawDir, '*.json')

ans =

    '/Users/battal/Documents/GitHub/CPPLab/CPP_BIDS_SPM_pipeline/demo/output/MoAEpilot/*.json'

Error using copyfile
cp: /Users/battal/Documents/GitHub/CPPLab/CPP_BIDS_SPM_pipeline/demo/output/MoAEpilot/*.json: No
such file or directory

Error in bidsCopyRawFolder (line 44)
    copyfile(fullfile(rawDir, '*.json'), derivativeDir);

Error in batch_download_run (line 89)
bidsCopyRawFolder(opt, 1);

[Remi-Gau]

OK will have into this tomorrow

[Remi-Gau]

• create a test for bidsCopyRawFolder

[CerenB]

I usually initiate matlab from command + space but this problem persisted when I initiate it from terminal window as well.
in bidsCopyRawFolder.m in the section of:

try
        system( ...
          sprintf('cp -Lr %s %s', ...
          fullfile(rawDir, subDir), ...
          fullfile(derivativeDir, subDir)));
      catch
        message = [ ...
          'Copying data with system command failed: are you running Windows?\n', ...
          'Will use matlab/octave copyfile command instead.\n', ...
          'Could be an issue if your data set contains symbolic links' ...
          '(e.g. if you use datalad or git-annex.'];
        warning(message);
 
        copyfile(fullfile(rawDir, subDir), ...
          fullfile(derivativeDir, subDir));
      end

does not copy the subject folder. Without -L option, it works. with -Lr option it provides:
cp: the -H, -L, and -P options may not be specified with the -r option.

[marcobarilari]

I think we can close this one

[Remi-Gau]

@all-contributors please add @CerenB for bug