[Homer-users] nasty bug with changing spatial units

[David Boas]

Dear All,
We implemented the SD.SpatialUnit field a few months ago so that it is 
explicitly stated in the data structure what the spatial units are. It 
became necessary to implement this as we prepare to roll out the 
atlasViewer for using a brain structure to guide interpretation of the 
fNIRS data. We just found a nasty little error that we have fixed. It is 
likely that this error has affected some of you and I wanted to tell you 
what it does.

Please note, that Homer2 prefers to work with mm spatial units. This is 
the convention that we are using for atlasViewer.

If you run Homer2 to process a group of .nirs files that have not yet 
been initialized with SD.SpatialUnit, then Homer2 indicates such and 
asks you for the spatial units. If you indicate that SD is currently in 
cm units and agree to convert it to mm units then the first file 
converted is correct, the second file converted gets a number 10x larger 
making it units of 0.1mm, the third file gets another 10x making it 
units of 0.01 mm, and so on. The result is that in your conversion to 
concentration units you are likely to see smaller and smaller responses 
depending on which file you are looking at.

If you suspect that you have this problem, you can easily verify it by 
loading the .nirs file in matlab and examine SD.SrcPos and SD.DetPos and 
SD.SpatialUnit. Presumably SD.SpatialUnit = 'mm'. In that case, does 
SD.SrcPos and SD.DetPos also appear to be in mm units. If not, you can 
correct the numbers by dividing by 10 or 100 or whatever it takes to 
make it mm units. You can then save the .nirs file with the corrected SD.

Please let me know if you are having problems with this.

Thanks and sorry for the trouble.

David Boas