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BRAINSia / MiniPig

This is a private repository to manage the scripts and documentation for the MiniPig HD Project
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Shared Workspace #4

Closed Schubisu closed 9 years ago

Schubisu commented 9 years ago

Hi all, I've tried to upload the atlas files yesterday. However, our average upload is ~90KiB/s, so this took some hours just for github to tell me that the server rejected the files.

Additionally files above 100MB cannot be uploaded to github. This affects most of our 3D T1 nii.gz files.

I've reset my local git commits now and will try to upload at least the most important files. I have to wait till evening though, since any upload is totally blocking our network :/

Frauke will ask her radiology professor for a file server solution in their institute, since they have a fast fiber connection. We're not sure if and how we will be able to access the network from outside the university yet.

Schubisu commented 9 years ago

Just recently a new cloud project for scientific use has been established here and luckily the university of muenster is participating. We’ve uploaded the data there (in no time) and hopefully this will fulfill our needs.

You can access the directory here https://uni-muenster.sciebo.de/public.php?service=files&t=6e06840a0c338fb177776d1a96176636 password: minipig_HD_100

You should have download and upload rights.

I’ve uploaded all files of the french domestic pig atlas and the datasets of the two pigs that have a manually created whole-brain-mask already.

dmwelch commented 9 years ago

We're having issues with downloading at the folder level (we can download individual files fine).

unzip ${FILE}.zip

returns

zipfile claims to be last disk of a multi-part archive;
  attempting to process anyway, assuming all parts have been concatenated
  together in order.  Expect "errors" and warnings...true multi-part support
  doesn't exist yet (coming soon).
error [central structures.zip]:  missing 8538699678 bytes in zipfile
  (attempting to process anyway)
error [central structures.zip]:  attempt to seek before beginning of zipfile
  (please check that you have transferred or created the zipfile in the
  appropriate BINARY mode and that you have compiled UnZip properly)
Schubisu commented 9 years ago

The zip file should be okay, I'm able to unzip correctly. Here is a similar problem, maybe updating unzip helps?

http://apple.stackexchange.com/questions/149080/how-can-i-update-my-version-of-unzip-to-version-6-00-or-higher

I'm no OSX user but this tool may help you with large-file support: http://wakaba.c3.cx/s/apps/unarchiver.html

dmwelch commented 9 years ago

unzip via brew does not support large-files: :exclamation: need PK compat. v4.5 (can do v2.1)

Solution was to run brew install p7zip and extract à la: /usr/local/Cellar/p7zip/9.20.1/bin/7z x -o${OUTPUTDIR} ~/Downloads/M340P100_20131031.zip