Hi Janine,

There can be multiple things in play:

• https://github.com/Neural-Systems-at-UIO/QuickNII-extras/blob/master/Java/PackWHSRatV4Demo.java#L218 tells the total number of (byte) volumes present in the file (it's 7 for this rat: 2 for MRI -16 bit grayscale-, 3 for DTI -24 bit RGB-, and 2 for the segmentation -16 bit indexed-, in this order)


• the modality headers contain volume indices: https://github.com/Neural-Systems-at-UIO... says MRI starts with 0 (its type in line 61 above defines it's 16-bit grayscale), then line-pair 77-82 specifies the DTI (starting at volume index 2), and lines 86 and 92 tell about the segmentation.

Nice job packing the atlas with so little documentation, and I hope these points will help with the final cleanup.
We have a very tiny editor for the description text that appears in the about box, should you need one: https://www.nesys.uio.no/QuickNII-About/ is its location (it opens a cutlas file, and then saves the result into the download folder of the browser, usually).

Cheers,
Gergely