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aces / brainbrowser

Web-based visualization tools for neurological data.
https://brainbrowser.cbrain.mcgill.ca/
GNU Affero General Public License v3.0
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Brainbrowser v 2.5.2 has issues loading minc files from some scanners #332

Closed MounaSafiHarab closed 7 years ago

MounaSafiHarab commented 7 years ago

Tested on the brainbrowser website (volume viewer). Loading the minc file directly does not work and gives the error below: "Sorry, this does not look like a NetCDF file." Loading the header and raw files work without a problem. The file comes from a Philips scanner.

p.s: I am using a dcm2mnc binary provided to me by @rdvincent (that solves issues with GE and philips scanners we have encountered in the past) to generate the minc files (in case this info is of relevance).

rdvincent commented 7 years ago

@MounaSafiHarab This is probably an HDF5 file using some new feature or version that the existing HDF5 reader doesn't support. Can you send me an example?

MounaSafiHarab commented 7 years ago

@rdvincent

Sure. I sent you a separate e-mail with details of where I placed some example files for you. Thanks!

rdvincent commented 7 years ago

@MounaSafiHarab Hi, I have looked at this problem and it seems to have been fixed after 2.5.2 was released. Perhaps @natacha-beck could make a 2.5.3? I think this commit is probably the one that fixed the issue: 662e23c4e4a5bcf111a2b6d0e9fc7d53626db31c

natacha-beck commented 7 years ago

@rdvincent and @MounaSafiHarab just done a minor release 2.5.3 that include this fix.

But Mouna still have issue:

so the new brainbrowser fixed the viewing of almost all files except the DTI ones still issue the same error for me so all anatomical (t1, t2) and all fMRI are good

MounaSafiHarab commented 7 years ago

I have put 2 dti sample files that still have this issue in a directory that I will send you the path for in an email.

rdvincent commented 7 years ago

@MounaSafiHarab @natacha-beck Thanks I should be able to look at it soon.

natacha-beck commented 7 years ago

@MounaSafiHarab @bert I star to take a look to this issue, Apparently it is a HDF5 file but BrainBrowser failed to find the xspace, ysapce and zspace (I can get this information with mincinfo). Then it try to read the file as a NetCDF and failed since it is a HDF5.

rdvincent commented 7 years ago

@natacha-beck @MounaSafiHarab I have added a commit to my fork that should fix these files, I will do a pull request soon.

MounaSafiHarab commented 7 years ago

thanks @rdvincent @natacha-beck

problem resolved in 2.5.4!