NITRC QuickNII - Serial section aligner to volumetric atlases Forum: general

RE: Image Data Export

Cooper Payne — Fri, 05 Jun 2026 14:13:06 GMT

Hi,
I will double check with my team, but that appears to be exactly what we were looking for! Brilliant!
Thank you so much for the assistance!
Best regards,
Cooper Payne

RE: Image Data Export

Gergely Csucs — Fri, 05 Jun 2026 11:22:34 GMT

Hi,
https://www.nesys.uio.no/QuickNII/coordinates.html may be doing what you ask for. It allows you to select a QuickNII series descriptor (JSON format is supported only), and then it immediately attempts to "download" an Excel file containing the coordinates in question. Because of this aspect the file will likely appear in the downloads folder of the browser.
I hope this helps, best regards,
Gergely

RE: Image Data Export

Cooper Payne — Thu, 04 Jun 2026 11:18:05 GMT

Hello, we are using QuickNII with the rat atlas WHSRat-v4.
We use image series for mapping recording these values for each image in the series compared across multiple brains may prove useful to be able to compare deviations.
Ideally, we would like to be able to take down all of the transformations in this atlas that is:
voxels, WHS (mm), bregma (mm), lambda (mm), WHS (voxels), bregma (voxels).
 
Best regards,
Cooper Payne

RE: Image Data Export

Gergely Csucs — Tue, 02 Jun 2026 10:37:10 GMT

Hi,
Those coordinates are the midpoints of the given images, so they also incorporate deviations coming from where/how the tissue sample is located/oriented on the slide. Unfortunately it's not easy to see where they point to: when you launch QuickNII, but don't load an image series, hovering the mouse over the values and control box makes a crosshair appear, that's where the coordinates come from.
Anyway, assuming that part is okay for your use case, yes, it's straightforward to create a utility that produces those coordinates. Would you mind naming the atlas in question, and if you have a preferred set of the transformations (some atlases have many of them)?
Best regards,
Gergely Csucs

Image Data Export

Cooper Payne — Mon, 01 Jun 2026 15:14:49 GMT

Hi, I am currently looking to see if there is any way to export the image data in the table that is nested under the 'values and control' window. That is, the transformation, x, y, and z coordinates. We would like to use this data for our project, however recording numerous values for 30+ images per hemisphere is not quite feasible.
 
Thanks for any help!

RE: Using a Custom Atlas in QuickNII

Gergely Csucs — Mon, 24 Nov 2025 11:32:44 GMT

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/QuickNII-extras/blob/master/Java/PackWHSRatV4Demo.java#L67 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

RE: Using a Custom Atlas in QuickNII

Janine Reinert — Sun, 23 Nov 2025 19:10:36 GMT

Dear Gergely first off: thank you very much for the fast help! So very quick. With your hints I managed to actually produce a working *.cutlas file with the inia19 dataset. The last thing I'd like to do (if possible) is to remove the DTI data from the file as we don't need it for registration and most monkey datasets don't even come with DTI data. However, if I don't include it in the cutlas, QuickNII throws an 'Array out of bounds' error so I'm guessing it will always expect the *.cutlas file to have 7 volumes total in the original order (i.e. 2 volumes MRI, 3 volumes DTI, 2 volumes Segmentation)? Cheers Janine

RE: Using a Custom Atlas in QuickNII

Gergely Csucs — Wed, 12 Nov 2025 16:09:00 GMT

Fiji is correct, the volume itself is 16-bit, but it contained 8-bit values only, and the example encoder knew about this.
Now there's a PackWHSRatV4Demo.java file too.
Looked at the inia19 dataset, and generally it will work with QuickNII, as the most important restriction of QuickNII is the isotropic voxel size. Smaller hiccups are expected though: the label file format is different from ITK (so a modified parser is needed), and the orientation is LPI (axis order matches, but all axes are in the opposite direction compared to what QuickNII will display).

RE: Using a Custom Atlas in QuickNII

Janine Reinert — Wed, 12 Nov 2025 9:55:14 GMT

Probably a mistake on my part relying simply on Fiji. At least there, both V2 and V4 are shown as being 16bit but the value ranges are indeed very very different. As this was more or less just meant as a trial to see if I can get QuickNII running with a 'custom' segmentation: do you think it can work with i.e. the data provided here: https://www.nitrc.org/projects/inia19?

RE: Using a Custom Atlas in QuickNII

Gergely Csucs — Tue, 11 Nov 2025 18:39:22 GMT

The WHSv4 atlas has 16-bit identifiers now (while piecewise they still would fit into 8 bits, their value range goes beyond 500 already). That's quite the change, I'll try to post an updated example tomorrow.