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aces / Loris-MRI

The set of scripts that preprocess and insert MRI data into the database.
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[bids_import] Images not found after import #969

Closed jeffersoncasimir closed 1 year ago

jeffersoncasimir commented 1 year ago

While testing bids_import.py (#923), I encountered an issue with MRI.

I imported this dataset and it ran without errors. However, the following warning appeared: /opt/eegnet/bin/mri/python_virtualenvs/loris-mri-python/lib/python3.6/site-packages/nilearn/image/resampling.py:531: UserWarning: Casting data from int32 to float32 warnings.warn("Casting data from %s to %s" % (data.dtype.name, aux))

After selecting native for example from the session browser, the session viewer loads with broken thumbnails, shown below

Screenshot 2023-05-02 at 2 20 23 PM

When clicking a thumbnail, it loads /brainbrowser/?minc_id=[:id] and shows the message below:

Screenshot 2023-05-02 at 2 20 43 PM

There are no errors in the server log either.

cmadjar commented 1 year ago

@jeffersoncasimir what are the permissions of those files on the filesystem? Can they be read by apache? Are they located on the filesystem and can you open them outside of LORIS?

jeffersoncasimir commented 1 year ago

@cmadjar I just changed ownership to lorisadmin:www-data and tried without success with 777 permissions. The .nii files are on the filesystem and I downloaded one (using scp; 404 with download button) and I am able to view it and interact with it using this: https://socr.umich.edu/HTML5/BrainViewer/

jeffersoncasimir commented 1 year ago

I ran the same dataset with the test-25 VM and it works as expected. It appears to be an issue with my other VMs environment.

jeffersoncasimir commented 1 year ago

Please close this if you think it is no longer relevant.