How to annotate white matter channels for SEEG data

Hi, iEEG epilepsy researcher here. I wanted to ask about how to best annotate white matter and other channels that might not be part of your interest. Other examples include: out, csf, ventricle. Ideally there is a place to annotate this within the BIDS layout for iEEG data. This specifically comes up for SEEG (depth electrodes).

Currently iEEG-BIDS channels.tsv file has “status”, which is constrained to “good/bad”, and status_description. Would this be the right data points to modify to account for that?

If not, where else can this go?

-perhaps @sappelhoff

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Hi @adam2392

If I understood your question correctly, you would like to add data information per channel to the channels.tsv file.

As is usually the case in BIDS, you can add any number of arbitrary (i.e., custom) columns to your TSV files. See this part in the specification:

An arbitrary number of additional columns can be added. Those allow describing other properties of events that could be later referred in modelling and hypothesis extensions of BIDS.

The only important aspect of this is, that each custom column in the TSV files needs to be described in an accompanying JSON file. For example, look at this TSV file:

In there, we have a custom column “handedness”. To unambiguously describe what this means, there is an entry in the accompanying JSON file:

You could do the same for your case.

cc @Dora_Hermes

The location of the electrodes and therefore the properties of the tissue at the location should actually be noted in the _electrodes.tsv file. If you add custom columns this should indeed be described in an _electrodes.json file as indicated by @sappelhoff

Properties of the amplifier and recorded signals are stored in the _channels.tsv If a recorded channel has a bad signal because it is in the csf, this can be described in the _channels.tsv file. The reason for this is that BIDS makes a clear distinction between electrodes (hardware contacts at a certain position) and channels (signals recorded by the amplifier).

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Hi all,

I was validating our dataset with the BIDS validator, and got this error:


dataset descriptor/electrodes.json


Files with such naming scheme are not part of BIDS specification. This error is most commonly caused by typos in file names that make them not BIDS compatible. Please consult the specification and make sure your files are named correctly. If this is not a file naming issue (for example when including files not yet covered by the BIDS specification) you should include a “.bidsignore” file in your dataset (see for details). Please note that derived (processed) data should be placed in /derivatives folder and source data (such as DICOMS or behavioural logs in proprietary formats) should be placed in the /sourcedata folder.



I got the same error for events. tsv.

Both files are at the level mydataset/events.json and mydataset/electrodes.json. Do you have any recommendations what is causing this error?

Thanks for helping out!


At the same time, I made this electrodes.json to resolve this error (which does not work yet, since I still have this error…):

sub-RESP0521_ses-1_electrodes.tsv 17.124 KB |


dataset descriptor/sub-RESP0521/ses-1/ieeg/sub-RESP0521_ses-1_electrodes.tsv


Tabular file contains custom columns not described in a data dictionary


Columns: silicon, soz, resected, edge not defined, please define in: /electrodes.json, /sub-RESP0521/sub-RESP0521_electrodes.json,/sub-RESP0521/ses-1/sub-RESP0521_ses-1_electrodes.json,/sub-RESP0521/ses-1/ieeg/sub-RESP0521_ses-1_electrodes.json