BfNIRS Documentation

Request permission to create datasets

  • If this your first time creating a BIDS compatible fNIRS dataset on BfNIRS cloud, you need to accept terms and conditions before creating a dataset.
  • To accept terms and conditions, please click on Review and approve dataset upload terms of service button.
  • That will pop open terms and conditions, please scroll down and click checkbox to accept terms and conditions and close the window.
  • Then click Request Permission to create a Dataset button. It will take you to another page, press Request Permission Button in that page. Then your dataset page will like below.
  • Once the request is approved then you will see New Dataset button like below. Please note that it will take 24-48 hrs to review and approve your request.

Create a BIDS compatible fNIRS dataset

  • Press New dataset button create a new dataset.
  • It will ask you to enter a dataset name. Please enter appropriate name for the dataset.
  • A folder with your dataset name will be created.
  • To edit dataset please press Edit dataset button on top right corner.
  • Please note that only person can edit dataset at a time. So once you finish editing dataset please press Release lock button on the top left so that others can edit your dataset once you share dataset with others.
  • To create a subject folder in the dataset, click on Add Folder dropdown menu. It gives option to create subject and other folder option. Please click on subject folder radio button and enter you subject name. Subject folder has the sub-<label> format, in the name field sub- already pre filled for you. So please enter appropriate unique label for each subject. Subject label is alphanumeric, it contains only letters and numbers but not any special characters.
  • To add session folder inside the subject folder, please follow the similar procedure as above. You need session folder if you have multiple sessions for the subject.
  • Create a nirs folder inside the session folder or in subject folder if you don’t have a session folder inside the subject folder. To create a nirs folder, click on Add Folder dropdown menu, select nirs radio button. It will automatically creates the name for the nirs folder because this folder name should contain anything other than nirs.
  • Next to nirs folder, click on upload files and select snirf file to upload.
  • If the snirf file doesn’t have appropriate naming to be BIDS compatible, it will be in red color and you can hover over question mark symbol next to snirf file to see naming instructions for a snirf file. I addition to this, if you click on generate BIDS files button to generate BIDS metadata files, before generating metadata files you can see instructions to change the name of the snirf file and some of the name will be automatically filled and gives option edit rest of the name.
  • After changing the name, if you click on Generate BIDs files, metadata files required for BIDS will be created automatically.
  • Information in these metadata files is extracted from the uploaded snirf file. Snirf file contains most of the required most of the required metadata information but not all the required metadata information to create BIDS compatible metadata files. This information can be added manually.
  • To find all the missing metadata information, click on Validation Errors tab. This displays all the required missing information for each file. It displays type or error, filename, location and reason for the error. To edit the file, click on the filename to display the file to edit.
  • In the above error, NIRSCoordinateSystem key in the _coordsystem.json file is empty but this should not empty for the dataset to be BIDS compatible. After adding the correct information and saving the file, this error will be removed from Validation Errors. Like wise all errors can bed edited manually.
  • Above particular error (NIRSCoordinateSystem error) is very common as most of the snirf files does not contain this information. To add correct value for this, please refer to FAQs which contains more information about this error.
  • You can also generate quality report for the acquired data which gives quality repots for the acquired data.
  • To generate quality report, click on Generate Quality Report next to snirf file. After quality report generation, you can see view quality report link next to snirf file. If you click on the link, this will open quality report in a new window.