I am using an open-access FNIRS dataset for my research work. The dataset link is https://doc.ml.tu-berlin.de/simultaneous_EEG_NIRS/. I want to use this data in Brainstorm. A similar type of issue is already discussed at FNIRS data import - #4 by edelaire. In the earlier discussion, author [edelaire] suggested importing one .matlab script (shin_import.m). But I cannot import that script into Brainstorm.
Could you please help me with this topic?
@edelaire, any idea on this topic?
which script did you use? I think Jimmy applied some corrections to my original script: FNIRS data import - #9 by Jimmyuba1 .
You will need then to indicate the path to the data and execute the script.
I think i will need some details on the error you are facing to provide more help.
Also, If by any chance you manage to contact the author and have the data shared in the more standard format (BIDS?) and with the optodes coordinates, that would be great
I have used the modified script of Jimmyuba1. Initially, I tested for two subjects, and after resetting the folder path, # subjects, I got the attached error. The modified script is also attached to this mail.
import_modified.m (8.9 KB)
Please help me in this regard. Is the two subjects' data converted into .nirs format within the NIRS protocol in Brainstorm after the successful execution of the script?
this function is from NIRSTORM. make sure you have it installed and loaded using Brainstorm plugin system.
It's not exactly converted as nirs but just loaded into Brainstorm. I guess you could then export to nirs or snirf to use it more easliy in other software.
Thanks, Edelaire. Now it works.
I am using open-access NIRS data (https://doc.ml.tu-berlin.de/simultaneous_EEG_NIRS/) for my research. I have installed the "NirsStorm" plugin in BrainStorm and used the Hb/Hb_02 data extracted from NIRS signals (from the above link). When I click on "compute the head model" it shows "No head model found". So, I cannot proceed. The NIRS channels are 108.
Please look into the issue.
Unfortunately, head models can only be computed for either raw data or optical density as it requires information about the used wavelength. Once the data are transformed into concentration, the head model cannot be computed.
Additionally, the head model requires information about the position of the source and detector which also lack in this dataset.
hs: It might be a language issue but I find the tone of the sentence "please look into the issue' a bit strong. I am providing help on this forum outside of my working hour and am not working for you. Hence giving orders seems a bit out of line...
Thank you, @edelaire, for your input, continuous support, and help in the forum; we really appreciate it.
You are one of the bst-NIRS experts and the reference for all the questions the Brainstorm team can't answer.
I believe the comment from @ddaschakladar is just a miscommunication due to language; I'm also facing similar issues from time to time since English is not my primary language
Thanks a lot for your valuable comment. I am on vacation, so sorry for the late reply. It's a miscommunication and language issue. Strongly apologize for my mistake. I am seeking help with NIRS processing as I am new to this topic.