Exporting/Import BIDS Dataset

1

Hi Francois,

About exporting to BIDS
I am using the 'Export BIDS dataset [experimental]' process which creates two files per recording (a JSON and the .eeg file). The BIDS validator indicates there is multiple errors in the JSON file ('should not have additional properties')

When importing a BIDS dataset
I tried reimporting the BIDS dataset in a new protocol but it did not work. The error is that it cannot open the VHDR file (see screenshot). Is it possible to import a BIDS dataset that have .eeg file but no .vhdr/.vmrk files ?

Thanks for your help,
Corentin

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2

This process is a draft that has not be continued since 2019, it addresses a very limited amount of cases and does not fill a lot of the metadata fields.
It is part of our objectives to develop this capacity of Brainstorm to create valid BIDS dataset, so until we get time to work on this more formally, we will limit our developments to fixing the bugs reported by users.

I tried to fix the issues you reported here: https://github.com/brainstorm-tools/brainstorm3/commit/115b3987fcb6ccb1779330d19ee62a2d152cc61f

Please update Brainstorm, try again, and if you get new errors please report them here.

3

Hi Francois,

Thanks for updating Brainstorm.

There is one minor issue. The .vhdr and .vmrk files are indeed created, but they have the original name of the recording, not the bids name sub-XXXX_ses-XXXXXXXX_task-_run-XX_eeg. This causes an error since the .vhdr and .vmrk files are not found (they have a different name than the .eeg file.)

Thanks!
Corentin

4

Oops, sorry about that.
Fixed: https://github.com/brainstorm-tools/brainstorm3/commit/c58cec1325713367ebe690f4e1e0811fbf9ddca0

5

Hi François,

I have a follow up question on exporting/importing BIDS. I tried importing a BIDS and exporting it.

The original BIDS dataset has 2 subjects. Each subject has 1 session. Each session has 2 runs.

I have no problem when importing the BIDS dataset. When I export it, the resulting BIDS dataset is different. I still have 2 subjects, but each subject has 2 sessions (not 1).

The first session contains the first run with a valid file names (sub-0001_ses-XXXXXXXX_task-name_run-01_eeg.eeg).

The second session contains the second run with a different file name (sub-0001_ses-XXXXXXXX_task-sub00001sesXXXXXXXXtaskname_run-01_eeg.eeg). It concatenates the string 'sub-0001_ses-XXXXXXXX_task' to the file name that already contains this information.

I was expecting to have the exact same dataset, meaning that the files in the second session should be in the first session with valid file name.

Is this behavior normal ?

Thanks for your time,
Corentin

6

The process "Export BIDS dataset" is an experimental feature developed by one imaging center for helping them organizing their MEG acquisitions.
At the moment, I would not consider it a reliable option to export a Brainstorm database to BIDS.

Note that in Brainstorm we have to way to keep track of the difference between sessions and runs. One folder is exported as one session, since this is more versatile.