Unable to upload dataset to OpenNeuro

spinal-cord-7t / coil-qc-code

7T Spinal Cord Coil QC Analysis Code

https://spinal-cord-7t.github.io/coil-qc-code/README.html

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Unable to upload dataset to OpenNeuro #15

Closed Kyota-exe closed 7 months ago

Kyota-exe commented 9 months ago

OpenNeuro does not accept the dataset as it is, raising errors. Currently, the dataset is stored in Google Drive.

Since there seems to be issues in the dataset (#12, #13), we should probably resolve those first before attempting to fix the problems preventing the dataset from being uploaded to OpenNeuro.

evaalonsoortiz commented 9 months ago

Is there any additional information about which files are not BIDS compliant?

For issue #12 : As mentioned in the issue (https://github.com/spinal-cord-7t/coil-qc-code/issues/12#issuecomment-1952473648), the notebook should retrieve all 3 DREAM scans and combine them. This means that the DREAM scans with 3 different voltages should be included in the OpenNeuro dataset. However, it doesn't look like the lower and higher voltage scans were converted to BIDS (see my comment here: https://github.com/spinal-cord-7t/coil-qc-code/pull/9#issuecomment-1952548438). This issue should not stop us from making sure that the data we already do have is properly BIDS formatted.

For issue #13 : The correct NYU scans can be sorted out independently of the BIDS conversion issue.

Kyota-exe commented 9 months ago

Unfortunately, OpenNeuro doesn't give us much information on what exactly is wrong about the naming. Expanding the error simply enumerates all the files (111 files) and reiterates the error message:

The second error is easily fixable by adding an appropriate dataset_description.json file however, which I will do.

evaalonsoortiz commented 8 months ago

But we know that the file that is causing the problem is "sub-MGH1_acq-coilQaSagLarge_SNR.nii.gz, yes?

evaalonsoortiz commented 8 months ago

Is the suffix "coilQaSagLarge_SNR" part of BIDS?

evaalonsoortiz commented 8 months ago

After reading the acq- entry https://bids-specification.readthedocs.io/en/stable/appendices/entities.html#acq, I see that "coilQaSagLarge" is your label, and that "SNR" is a suffix. This must be what is causing the problem. @jcohenadad had pointed out in this comment: https://github.com/spinal-cord-7t/coil-qc-code/pull/9#pullrequestreview-1811994832 that "SNR" is not a BIDS suffix and had advised you on how to proceed in order to decide how to handle this file.

Kyota-exe commented 8 months ago

But we know that the file that is causing the problem is "sub-MGH1_acq-coilQaSagLarge_SNR.nii.gz, yes?

This is just the first file for which this error applies, there are in total 111 files that have filenames that don't comply with the BIDS convention (according to OpenNeuro at least).

Kyota-exe commented 8 months ago

I have created a new topic on NeuroStars asking for feedback and listing the scans for which the filenames are detected as incorrect on OpenNeuro.

Kyota-exe commented 7 months ago

Closing this issue as I no longer have any problems uploading the dataset on OpenNeuro.