fNIRS 3-D Reconstruction using CBSI Preprocessing

Discussions
1

Hello Brainstorm Team,

I’m currently working on fNIRS data preprocessing using Homer3 and performing 3-D reconstruction in BST. I would like to incorporate the Correlation-Based Signal Improvement (CBSI) method into my pipeline to correct for motion artifacts.

CBSI requires calculating hemoglobin concentrations before applying the method, so I compute the concentrations in Homer3, apply CBSI, and then convert the data into SNIRF format for use in BST.

However, I’ve encountered a challenge. For now when performing 3D reconstruction, we provided BST with the Differential Optical Density (dod) data from Homer3. The dod data is then converted automatically to hemoglobin concentrations during the source reconstruction (we used wMNE for now). Since CBSI needs to be applied to the concentrations beforehand, this built-in conversion conflicts with my preprocessing workflow.

Question: Is there a way to import already-preprocessed hemoglobin concentration data (post-CBSI) into Brainstorm and bypass its internal DOD-to-Hb conversion during source reconstruction?

Thank you for reading my post and any help is greatly appreciated :slight_smile:

-Mica

2

Ping @edelaire

3

Hello,

if you can export your data as snirf; it's supporting pre-processed data; then you should be able to import those to Brainstorm. You might need to ask homer people how to export processed data to snirf; Feel free to share the snirf file here; if you encounter any issue during the importation step.

Another solution, would be to add a custom process in brainstorm, to apply the CBSI and do all the processing inside brainstorm. i might be able to assist with that; but i will be quite busy over the next few month

Edouard