Hello,
Im using data from Nirx.
I created contrasts for each subject, but when plugging them into the 2nd level analysis in spm12, I noticed that all channels were being used for the calculations, including the short channels, even though I specified which channels to exclude in the subject-level. I wrote a code for plugging processed data from Homer3 to spm-fnirs (so that I can use Homer's processing stream instead of the original processing). We had an idea to eliminate the short channels from this data (create a smaller matrix), but since spm-fnirs uses other input files like the csv and HDR files, I'm sure how to treat them. For example, I'm not sure if I need to re-number the channels (so that there aren't any gaps in the numbers) or keep their original numbers.

Any help would be much appreciated.