Missing region IDs

Technical
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1

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!!

2

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?

3

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

4

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.

5

Dear all, is there any news on this issue? I also encountered this problem when using FIJI to open the 32bit annotation nrrd file. I have tried to trace the brain areas back that then had a wrong annotation ID but unfortunately you get multiple brain areas that then have the same atlas annotation. Is there a workaround such as opening the nrrd file in a different programm, then converting it to tif and then opening it in FIJI? Thanks for your input. Best, Constanze

6

Hello. I’m sorry but I don’t know what FIJI is doing with these .nrrd files. It does appear that FIJI thinks the range of values in the file is much, much greater than the maximum value of the structure_id in the annotation file. The values should be much less than the limits for a signed 32-bit integer. You may consider opening an issue with fiji or scifio ?

7

Thanks for your answer! Really strange indeed. Yes, I will do that. In the meantime, could you recommend an alternative to FIJI for opening the annotation file correctly?

8

Our go-to program for working with these files is ITK-Snap