[WIP] NIRX Probe Setup Importation
This wiki page is particularly tailored for NIRX users and will help to import your probe information into Nirstorm to enable powerful visualizations on your data and setup sensitivity. Please make sure that you already have a decent understanding of nirstorm/brainstorm and completed the provided tutorials. Please note that this tutorial is only provisional. We will provide a more suitable and easier option to integrate probe setups for NIRX users in due time.
To import your probe setup, you will have to provide your nirs data in .nirs format. If you have checked the respective check box in Nirstar before data acquisition, your data will be reformatted automatically into .nirs format right after data acquisition. However, if not, you will have to reformat your data first by following these steps (http://homer-fnirs.org/faq/#nirx2nirs) before proceeding with this tutorial.
For NIRScout and NIRSport devices, hemodynamic data (.nirs file) and probe information (.probeInfo file) are stored in separate files. The .nirs file will therefore contains incorrect values that do not represent your actual probe setup. Therefore, the actual coordinates need to be imported from the probeInfo file into your .nirs file, replacing the wrong values.
To do so, you just need to run the matlab file (ProbeImportNirx.m provided here: TO DO: download link) in Matlab and choose the respective .nirs and .probeInfo file of one exemplary subject of your experiment. Note that if you have changed your probe setup during your experiment, you will have to perform the following steps individually for each setup.
After running this function, you will find a second .nirs file named exactly like the old one plus a "_NIRSTORM" attachement. This .nirs file contains your hemodynamic data and the replaced probe information. However, there are still some further adjustments that need to be done within nirstorm as described in the following. You can rename that file more appropriately if you wish.
After you have loaded your new subject data (.nirs_NIRSTORM), you will see a NIRS BRS-channels file (assuming you have used the Colin27 template for NIRS). Richt-click on it > Display Sensors > NIRS (pairs). You will see your probe setup nearby the actual template but still a little bit messed up. Now you will have to adjust your probe setup to the head template manually. Right-click on NIRS-BRS channels again > MRI Registration > Edit. This Step will need quite a bit of time to adjust your model properly. In the upper pannel you can choose between linear or rotational movements around the x, y, or z axis. If you have sufficiently adjusted the probes to the headmodel you can click on "OK" and save your progress.
You can do this either with a self-written matlab script or organization program of your choise (such as meld), or by doing it manually. This step requires you to manipulate the brainstorm_db folder, which is highly unrecommended. Please make sure that you are aware of that and be attentive of the changes you will make. The probe information you want to access is stored here: brainstorm_db > "Name of your created project" > data > "subject name" > raw"subject name" > channel.nirsbrs.mat
Simply copy that file that you in your exemplary subject folder and replace it in every other subject folder. In brainstorm you will now have the appropriate head model for all participants. If you make further changes, brainstorm will ask you, if you want to transfer these changes to all other participants.
However, as stated above, this process is not recommended and only provisional. Feel free to contact us if needed and ask about the current state of progress.