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pyushkevich / itksnap

ITK-SNAP medical image segmentation tool
http://www.itksnap.org
GNU General Public License v3.0
300 stars 89 forks source link

ITK snap unable to open large files #146

Open PolarBean opened 1 week ago

PolarBean commented 1 week ago

for some reason it seems itk snap is either unable to open some large files or simply opens them as all gray volumes. for an example of a large volume which does not load on a machine with 256GB of ram see https://datadryad.org/stash/downloads/file_stream/182481 and for my own time series data which loads as a gray volume see: https://data-proxy.ebrains.eu/api/v1/buckets/space-for-testing-the-nutil-web-applicat/demba_dev_mouse_first_half.nii.gz

The first volume opens when i crop out some of the data and the second works when i crop the time dimension. Please let me know if I am missing something :) thank you

baishi commented 1 week ago

Hi PolarBean,

I believe itksnap is able to open moderately large files. We managed to load a few GB large files. However, we haven't tried the file as large as 7.8GB. I'm downloading and giving it a try. However, the major time during loading would be the gunzip process, which is not very efficient.

As for gray volume, you can switch to Cursor Inspector tool and Under the Intensity under curosr: table, right click the Layer row and select Multi-Component Display and select RGB and you would see the colours.

Hope that helps. Shi

PolarBean commented 1 week ago

Hi Baishi thanks for your reply. When I say the volume is gray I don't mean that it's gray but should be colour. I mean it fails to load the contents of the volume and shows as all zeroes. This only occurs when I have 27 time points. If I have 26 it loads normally. image