cpp-lln-lab/cpp_bids

a set of matlab / octave function to create BIDS comptible folder structure and filenames

cpp_bids's Issues

Update doc

• split into several files

Binder example

• initialization of extracolumns
• explain how to create the different JSON files
• save stim file
• save for EEG
• save for iEEG
• save for MEG

reuse spm_mkdir and spm_copy to facilitate creating and copying BIDS dir hierarchy

https://en.wikibooks.org/wiki/SPM/BIDS

add unit tests

• removeAllDateSuffix
• convertSourceToRaw

cfg setDefault usage

I always forget, and was looking in README for usage of functions. first we set values in our experiment setParams.m and then run CPP_BIDS functions (e.g. userInput and createFilename). createFilename will set fields IF it's not set previously. Right? So my cfg.fields should be filled before I call BIDS functions.

Would you like to add one sentence somewhere that first the user should run their getParams and set all the fields. Then empty fields would be filled by the default values in CPP_BIDS functions.. I can add it as well, if you can point out where that info should be? e.g. in usage notebook?

add github action, travis and other CI badges

Add support for EEG, MEG, iEEG, BEH

• create json file associated
• create BIDS valid dummy data sets
• manage modality specific suffixes

refactor JSON creating functions into one function

Allow to add data to JSON files on the fly when saving them

Add basic info on how to add this repo as submodule

save stim file

is it possible to create two different output file? e.g. .tsv file for stimulus and .tsv file for tapping

skip saveEvents when there is nothing to save

creating unasked folder

it might be my issue, will check but now the code is creating eyetracker folder in addition to beh folder.

createFilename input reordering

It calls createFilename(expParameters,cfg)
I'm proposing to be consistent with the rest of the scripts the following order change:
createFilename(cfg,expParameters)

Add licence

createFilename does not support the BIDS 'physio' 'eeg' 'meg' type

Unit tests

• check good saveEvent behavior when the first event is empty
• check warning behavior when an saveEvent has to deal with an empty event
• make sure trial type, onset and duration are properly init
• check warning behavior when an array is too long
• create tests for errors

returnNamesExtraColumns returns logfile but it has not been change

can it be deleted from the outputs?

ensure that date of creation in copyright matches file creation

Make functions more verbose

• mention directory and filename setting
• mention directory and filename creation
• mention file saving

set up a release protocol / checklist (see BIDS specs for ideas)

for example I forgot to update the version.txt in the last release

test to see if it shows up in the kanban project automatically

inccorect saved ouput by readAndFilterLogfile

@Remi-Gau and @marcobarilari this is still open issue right? I see the .tsv file is only producing 1-line instead of saving the full output structure. I see it's because of how readAndFilterLogfile is creating the data structure and how tsvwrite function reads, basically the dimensions do not match. the output readandFilterLogfile is size = 1, and tsvwrite goes through that size option.
The test_readAndFilter does not fail because it does not look at how .tsv file is saved - which is only saving the 1-line of the output.

Originally posted by @CerenB in #104 (comment)

update README with the correct CI badges

• update README with the correct CI badges

Originally posted by @Remi-Gau in #101 (comment)

create or update a scan.tsv file for each participant

At first let's not worry about the anonymization issues and let's keep the dates as they are.
https://bids-specification.readthedocs.io/en/stable/03-modality-agnostic-files.html#scans-file

Save JSON files

make trial_type not required

The BIDS specs only have onset and duration as required so make sure that saveEvents skips events with the wrong values.

set 0 as default value for `duration`

automate update of CHANGELOG when bumping version

see here for some starters: https://github.com/bids-standard/bids-specification/blob/c27f613c779ba75e35397576998ccf388cfb8943/.circleci/config.yml#L65

bids addpath

Atm, when the bids added with
addpath(fullfile(pth, 'lib', 'CPP_BIDS', 'src'));
due to the subfunc folder is not inside src, would it be an issue? Will check it now. (after resolving the following error)

Check suffix inputed by users for mri filenames (e.g. rec / acq / ce...)

Need to make sure they are purely alphanumeric eventually with camelCase.

saveEventsFile - warning

1. Warning
   It seems to be passing this warning when there's nan. But I think I still have nans - as early Xmas decoration in my response collection array, somehow. Thus I have 13 (number of button pressed) error messages like this:

Warning: Missing some target data for this event. 
> In saveEventsFile>checkExtracolumns (line 240)
  In saveEventsFile>checklLogFile (line 166)
  In saveEventsFile (line 84)
  In fMRIMainExperiment (line 229) 
           onset: 199.7325
      trial_type: 'response'
        duration: 0
        key_name: 'space'
         pressed: 1
          fileID: []
    extraColumns: []
          target: NaN

2. It does not separate the time of the date in the saving name:
   sub-001_ses-001_task-RhythmCategFT_run-001_events_date-202007272044.tsv previously it was:
   sub-001_ses-001_task-RhythmCategFT_run-001_events_date-20200727_2044.tsv
   Previous version was slightly easier for a human to read.

Update readme

Simplify use of saveEventsFile

Update contributing guide

use MOXunit and MOXcov for testing and coverage

https://github.com/MOxUnit/MOxUnit

https://github.com/MOcov/MOcov

add unit tests

• to check the different BOLD naming patterns

make createFileName accept 'beh'

I think at the moment we only accept pc but it would make sense to have beh as well I think. Feel free to open an issue so we remember to do that.

Originally posted by @Remi-Gau in #123 (comment)

transfer instructions to bids

json createDataDictionary overwrite

I'm opening two logfiles (_event and _stim) consecuitively. When I only open the logfile (_event) with extraColumn, createDataDictionary nicely creates a json file with all the extra columns.
Then when I open the following, _stim, that json file for the logfile / _event got back to its default settings without the extraColumns.

Any idea why is it happening?

    % create  logfile with extra columns to save - BIDS
    logFile.extraColumns = cfg.extraColumns;
    [logFile]  = saveEventsFile('open', cfg, logFile); %dummy initialise

    % set the real length of columns
    logFile(1).extraColumns.LHL24.length = 12;
    logFile(1).extraColumns.PE4.length = 12;

    % actual inititalization
    logFile = saveEventsFile('open', cfg, logFile);
    
    % create response file - used for counting button press
    responseFile.extraColumns = cfg.responseExtraColumns;
    responseFile  = saveEventsFile('open_stim', cfg, responseFile);

[INFRA] Error in CI on checking the markdown

Error in CI on checking the markdown

https://travis-ci.com/github/cpp-lln-lab/CPP_BIDS/jobs/430652513

$ npm install `cat npm-requirements.txt`

Unhandled rejection Error: EACCES: permission denied, mkdir '/home/travis/.npm/_cacache/content-v2/sha512/a4/f5'

Unhandled rejection Error: EACCES: permission denied, mkdir '/home/travis/.npm/_cacache/content-v2/sha512/33/9a'

Unhandled rejection Error: EACCES: permission denied, mkdir '/home/travis/.npm/_cacache/content-v2/sha512/ce/b2'

Unhandled rejection Error: EACCES: permission denied, mkdir '/home/travis/.npm/_cacache/content-v2/sha512/d2/66'

Unhandled rejection Error: EACCES: permission denied, mkdir '/home/travis/.npm/_cacache/content-v2/sha512/a2/ce'

npm ERR! cb() never called!

npm ERR! This is an error with npm itself. Please report this error at:

npm ERR!     <https://npm.community>

npm ERR! A complete log of this run can be found in:

npm ERR!     /home/travis/.npm/_logs/2020-11-08T10_35_52_601Z-debug.log

The command "npm install `cat npm-requirements.txt`" failed and exited with 1 during .

Originally posted by @Remi-Gau in #120 (comment)

Easier alternative to `mpm` to manage this repo inside other projects

see cpp-lln-lab/CPP_PTB#21

Create a binder for demo

userInput need else condition for subjectGrp variable

if askGrpSess(1)
        subjectGrp = lower(input('Enter subject group (leave empty if none): ', 's'));
    end

At the moment, outside of debug mode, there's no subjectGrp assignment if askGrpSess =0. So the script crashes there.

lower case in saveEventFile

is it compulsory for BIDS? If yes, then nothing can be done, I see. But if it's not having small letters all the way through does not help to read variables in logfile.

add contributors

@all-contributors please add @Remi-Gau code, design, doc

makes changes to adapt to the new version of the BIDS validator

Some of the rules on the requirements of the stim files have now been enforced in the new version of the bids validator.

https://github.com/bids-standard/bids-validator/releases/tag/v1.5.6

After I bump up version of CPP_BIDS I will try to have a look at that and let you know what it changes.

tagging @CerenB as you might want to follow up on that. 😉

consider making subjectGrp optional

in createFilename.m
at the current state, in userInput function I can leave the group part empty but then in createFilename gives error that
Reference to non-existent field 'subjectGrp'

make sure that BIDS output created passes BIDS validator

consider making eye-tracker optional

in createFilename.m

cannot save cell input

In SaveEventFile.m, I cannot save cell array. Is there a solution or suggestion for this?

Error using fprintf
Function is not defined for 'cell' inputs.

Error in saveEventsFile (line 86)
                   fprintf(logFile(1).eventLogFile, '%f\t', data);

Error in tapMainExperiment (line 102)
       saveEventsFile('save', expParam, currSeq, ...