This repo contains python source code for converting data files in the BIDS-NIRS-Tapping dataset from SNIRF format to NWB format using the ndx-nirs extension. The NWB files will be placed in a directory structure appropriate for upload to the DANDI archive.
Note: this repo is at a WIP stage. Improved organization, documentation, unit tests, etc are expected to be added with time.
$ pip install -r requirements.txt$ mkdir data
$ cd data
$ wget https://github.com/rob-luke/BIDS-NIRS-Tapping/archive/388d2cdc3ae831fc767e06d9b77298e9c5cd307b.zip -O BIDS-NIRS-Tapping.zip
$ unzip BIDS-NIRS-Tapping.zip
$ mv BIDS-NIRS-Tapping-388d2cdc3ae831fc767e06d9b77298e9c5cd307b BIDS-NIRS-Tapping
$ cd ..$ python convert_tapping_dataset_to_nirs.py data/BIDS-NIRS-Tapping data/dandiset_stagingThis will read in the snirf files and BIDS metadata from data/BIDS-NIRS-Tapping, and output the nwb files in a dandiset-appropriate filestructure inside of data/dandiset_staging. The input dataset path must already exist. If the output path does not exist it will be created.
For more usage information, you can execute:
$ python convert_tapping_dataset_to_nirs.py --helpThe currently implemented SNIRF -> NWB mapping is as follows:
/formatVersion->NWBFile.notes/nirs/data1/dataTimeSeries->NIRSSeries.data/nirs/data1/time->NIRSSeries.timestamps/nirs/data1/measurementList{i}/sourceIndex->NIRSChannelsTable.source/nirs/data1/measurementList{i}/detectorIndex->NIRSChannelsTable.detector/nirs/data1/measurementList{i}/wavelengthIndex->NIRSChannelsTable.source_wavelength/nirs/data1/measurementList{i}/dataType-> Checked but not mapped. Must have a value of1(Continuous Wave - Amplitude)/nirs/data1/measurementList{i}/dataTypeIndex-> Checked but not mapped. Must have a value of1/nirs/metaDataTags/SubjectID->Subject.subject_id/nirs/metaDataTags/DateOfBirth->Subject.date_of_birth/nirs/metaDataTags/sex->Subject.sex/nirs/metaDataTags/MeasurementDate->NWBFile.session_start_time/nirs/metaDataTags/MeasurementTime->NWBFile.session_start_time/nirs/metaDataTags/LengthUnit-> Checked but not mapped. Must have a value of'm'/nirs/metaDataTags/TimeUnit-> Checked but not mapped. Must have a value of's'/nirs/metaDataTags/FrequencyUnit-> Checked but not mapped. Must have a value of'Hz'/nirs/metaDataTags/MNE_coordFrame-> Not Mapped/nirs/probe/wavelengths->NIRSChannelsTable.source_wavelength/nirs/probe/sourcePos3D->NIRSSourcesTable.{x,y,z}/nirs/probe/sourceLabels->NIRSSourcesTable.label/nirs/probe/detectorPos3D->NIRSSourcesTable.{x,y,z}/nirs/probe/detectorLabels->NIRSSourcesTable.label/nirs/probe/landmarkPos3D-> Not Mapped/nirs/probe/landmarkLabels-> Not Mapped/nirs/stim{i}/name-> Not Mapped (equivalent info mapped from BIDS events tsv)/nirs/stim{i}/data-> Not Mapped (equivalent info mapped from BIDS events tsv)
Some additional data is mapped from BIDS metadata files:
dataset_description.json:"BIDSVersion"->NWBFile.notes"Authors"->NWBFile.experimenter
subj-{i}/nirs/subj-{j}_coordsystem.json"NIRSCoordinateSystem"->NWBFile.notes"NIRSCoordinateSystemDescription"->NWBFile.notes"NIRSCoordinateUnits"->NWBFile.notes
subj-{i}/nirs/subj-{j}_task-tapping_nirs.json"TaskName"->NWBFile.notes"PowerLineFrequency"->NWBFile.notes
subj-{i}/nirs/subj-{j}_task-tapping_events.tsv->TimeSeriesinNWBFile.stimulus
This dataset has been posted as dandiset DANDI:000122:
https://gui.dandiarchive.org/#/dandiset/000122
The full instructions for uploading a dandiset can be found here: https://www.dandiarchive.org/handbook/10_using_dandi/#uploading-a-dandiset
The DANDI documentation should be used as the source of truth. Below is a summary of commands used to upload the first draft of the dandiset (using dandi==0.26.1).
To print out information on the dandiset:
$ dandi ls -r https://identifiers.org/DANDI:000122
To validate the nwb files for use in a dandiset:
$ dandi validate data/dandiset_staging
Everything should pass.
Next, download the dandiset. This is even required for an empty dandiset, as it will download the metadata file and setup the directory structure.
$ cd data
$ dandi download https://dandiarchive.org/dandiset/000122/draft
Now we can use dandi to automatically reorganize the nwb files in the appropriate way. First we'll do it as a dry run just to verify the process.
$ cd 000122
$ dandi organize ../dandiset_staging -f dry
Note that this will automatically rename the nwb files according to a pre-defined schema. Execute dandi organize --help for more information.
If everything looks good, go ahead and let the reorganization actually run
$ dandi organize ../dandiset_staging
Assuming everything looks good at this point, the dandiset is ready to upload!
$ dandi upload
Note: these steps were used to upload the first draft of the nwb files. The process for updating with new nwb files is similar. The files which are to be replaced should be manually deleted before running dandi organize. All other steps are the same.
The following metadata was entered manually on the dandiset page:
Dandiset title: Human fNIRS recordings of motor cortex during finger-tapping taskDescription: This experiment examines how the motor cortex is activated during a finger-tapping task. Participants are asked to either tap their left thumb to fingers, tap their right thumb to fingers, or no cue is given (control). Tapping lasts for 5 seconds and is prompted by an auditory cue. Sensors are placed over the motor cortex as described in the montage section in the link below, short channels are attached to the scalp too. Further details about the experiment (including presentation code) can be found at https://github.com/rob-luke/experiment-fNIRS-tapping.License: spdx:CC-BY-4.0Keywords: fNIRS, Haemodynamics, Motor Cortex, Finger Tapping TaskDandiset Contributors: managed byOwnershipfieldRelated Resource:dcite:IsOriginalFormOf: https://github.com/rob-luke/BIDS-NIRS-Tappingdcite:IsDescribedBy: https://github.com/rob-luke/experiment-fNIRS-tapping