Missing region IDs

Sorry if this is a naive question, but I don’t understand the source of the inconsistency I keep encountering.

I’m trying to map my data to the CCFv3 in matlab. My code generates a list of positive pixels with a the corresponding region ID. Most of the hits make sense, but I also get a few regions IDs that I cannot identify. I generated my list of IDs by downloading all the IDs and region names present in the structure tree. When I also search the structure, I get a key error for the ID value.

Could someone please double check that these regions truly don’t exist in the structure? Some of the missing IDs I’ve gotten are 182305696, 182305712, 312782560, plus a few more…

Is there a better way to generate a comprehensive list of the region IDs that would include the ones I’m missing??

Thank you!!

Sorry, I’ve done a bit more troubleshooting and I think the problem already exists when I open the nrrd file in Fiji. For example, I see what I think is the supraoculomotor periaqueductal gray as 61445472 but this is actually 61445477 in the ID list. Fiji is reading this as a 32 bit file 528x320 pixels. Should I be reading this file differently?

Hello Marcela

Can you please tell us more about how you downloaded the structure ids and names? Indeed, structure id 61445477 refers to Su3, and there is no structure for 61445472. My reference is this API call:
http://api.brain-map.org/api/v2/structure_graph_download/1.json

Best regards,
Wayne

Hi Wayne,

Thank you for your response! I’m certain now that the problem is when I open the file in Fiji. If I open the nrrd in matlab, all IDs seem to match their corresponding regions.

I’ve downloaded the annotation both using this link http://download.alleninstitute.org/informatics-archive/current-release/mouse_ccf/annotation/ccf_2017/
or with python following this example:
https://allensdk.readthedocs.io/en/latest/_static/examples/nb/reference_space.html

I have tried just dragging the file to open in Fiji or importing as an nrrd. Both indicate in the image stack that they have opened as 32bit.