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Frequently Asked Questions

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katja heuer edited this page Apr 25, 2021 · 17 revisions

Welcome to the BrainBox Frequently Asked Questions

How do I host files so that they are accessible through BrainBox?

Use Zenodo, the Open Science Framework or FigShare. That way your files will have a stable URL and a DOI. People contributing to your project will not risk loosing their work, which would happen if you hosted your files on your Dropbox and then you removed them. In that case, the URL link used by BrainBox would be pointing to a file that doesn't exist anymore.

How do I make sure that my files are visible in BrainBox?

You open a private browser window, paste the url to your file, and if your file downloads automatically, it means it will be visible in BrainBox. In case you need to click any confirmation, it won't work (for example, when files on G-Drive are >30MB). For testing a single link, you can always just paste it into BrainBox's landing page and click Go.

How do I host and include files from Zenodo?

Your MRI files need to be hosted there as single files so that each of them has its unique URL. The repository needs to be public for BrainBox to see it. You can then copy the link address of the file and use it directly as it comes, no modification needed. For obtaining links to many files, use Zenodo's API.

How do I include files from Google Drive?

Once you uploaded your file into a G-Drive folder, you can

  • get the share link.
    • Make sure that "anyone with this link can view" the file.
    • Please be aware that if you later remove this file or change its location and its url, you and your collaborators will lose access to the annotations. This is because in BrainBox, annotations are linked to specific URLs.
  • the file needs to be smaller than 30MB, otherwise google will block the download
  • the link obtained from g-drive needs to be modified like this:
    • replace file/d/ by uc?id= and delete /view?usp=sharing at the end of the url
  • You can check that if you paste your url in a private window, the file should be downloaded to your computer – then it means it should work in BrainBox :)

How do I include files from Dropbox?

Once you uploaded your file to Dropbox, you can

  • get the share link, and you will need to modify it like this:
    • replace www by dl and
    • delete everything after nii.gz
  • You can check that if you paste your url in a private window, you should be able to download the file – this means it should work in BrainBox :)
  • Please be aware that if you later remove this file or change its location and its url, you and your collaborators will lose access to the annotations. This is because in BrainBox, annotations are linked to specific URLs.

What happens if I move or remove my files from G-Drive, Dropbox and other services where this operation is possible?

Please be aware that if you include files into BrainBox, and later remove this file or change its location and its url, you and your collaborators will lose access to the annotations. This is because in BrainBox, annotations are linked to specific URLs. So including the file again from a new location may not bring the annotations back if the link has changed.
If you really need to move files, please download all annotations before that (via BrainBox API using a python script, or using the download button for single file), then move your files, and in case the links changed, upload all annotations so that they will be associated with the new URLs.

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