For our experiment, we are in the process of MRI registration and digitizing our NIRS optodes so that we can eventually conduct spatial analyses with our data. We plan to create a spatial template that will be imported and applied to all of our participants' files in brainstorm.
At the moment, we are pre-processing data (marking motion/checking signal quality, applying filters, baseline normalizing, segregating file into different experimental trials, averaging trials). Can the spatial template be uploaded to all files AFTER pre-processing for them is done? Or will this result in having to redo our preprocessing steps?
Was hoping someone here would be able to shed some light on whether it is advisable to wait or whether we can continue.
Thank you!
I'm not sure I understand what you mean with "spatial template".
Do you refer to the anatomy (MRI + surfaces), or to the position of the optodes?
The reference MRI (= the first file imported) in the subject anatomy is the reference for all the spatial information available for this subject (surface, sensors, light sources, dipoles...). The positions of the NAS/LPA/RPA files define the SCS coordinate system in which all the spatial information is saved in the Brainstorm database.
https://neuroimage.usc.edu/brainstorm/CoordinateSystems
Changing the position of the NAS/LPA/RPA points after importing other files (surfaces, sensors...) requires updating all the other files, and there are no automated tools for doing that. It is possible to do it manually, but chances of making errors when applying transformation matrices are high, and this is therefore not recommended. If you have to change the anatomy of the subjects later, it is safer to re-import all the data after (surfaces, sensors, recordings...)
On the other hand, changing the coordinates of the sensors (saved in the channel files: https://neuroimage.usc.edu/brainstorm/Tutorials/ChannelFile#Edit_the_channel_file) after importing/preprocessing the anatomy and the fNIRS recordings in the database should not be a problem.
If you have estimated source maps, they need to be deleted and recomputed. But other than that, you can probably import/pre-process/average all the recordings, and then later add the positions of the sensors to the channel file in order to proceed to further spatial analysis.
Does it help?
@edelaire