Importing large neuroimaging data into Omero

I have a question about importing neuroimaging data into Omero, specifically nii.gz files. In this case I used a publicly available dataset from OpenNeuro.

I was able to use the command-line image importer to import fmap data with images on the size of about 2.2MB each. This worked relatively quickly.

I was also able to import func data, the image was around 375MB. However, that import took 26 hours. One core was used at 100% by the java process over that time period.

Is there a more efficient way to import the larger files?

Could you point us to the image you used? So we could try to replicate the issue.
Thanks!

Kind Regards,
Dominik

Great, thank you.

I used https://openneuro.org/datasets/ds002737/versions/1.0.1

Specifically this file:
sub-01/ses-01/func/sub-01_ses-01_task-Stroop_acq-cf1PA_run-02_bold.nii.gz

Which can be downloaded directly with this link:
https://openneuro.org/crn/datasets/ds002737/snapshots/1.0.1/files/sub-01:ses-01:func:sub-01_ses-01_task-Stroop_acq-cf1PA_run-02_bold.nii.gz

Thanks. I tried to import the image with Insight. Curiously the import of the unzipped image worked fine, took a few minutes, mostly because of the upload to the server. But the import of the same image as the original zipped nii.gz file is still ongoing, after an hour has passed already. We’ll have a look into what’s happening there.
Kind Regards,
Dominik

Hi Dominik,

Is there an update on this?

We’d like to setup a production instance of Omero in our facility, but this is a current blocking item.

Sorry, @gregjones. The GitHub issue referencing this thread didn’t get auto-linked:

The best current suggestion would be to uncompress the files before import.

~Josh