Hey Xin,

The .SD file contains information about the arrangement of sources and detectors and their wavelengths, if information in this file is not organized correctly then it may be giving you these problems.

The webpage http://homer-fnirs.org/faq/#nirx2nirs was very helpful to me, especially the "Format for .nirs file and sample .nirs files" section of the page. 

"There is a possible issue with the formatting of the measurement list, i.e. the variable ml which is the same as SD.MeasList. It is advisable that measurements be ordered by wavelength. ml is a Nx4 matrix where N is the number of measurements and each column describes the source index, detector index, data type index, and wavelength index for each measurement. While in theory the measurements can be ordered in any way, in practice it seems that some functions only work properly if all measurements for the first wavelength are ordered first, and then the second wavelength, and so on."

Hope this information is helpful. 

Best,

Katie