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templates download as empty nifti files #7

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switt4 opened this issue Oct 7, 2019 · 3 comments
Closed

templates download as empty nifti files #7

switt4 opened this issue Oct 7, 2019 · 3 comments
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@switt4
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switt4 commented Oct 7, 2019

Hi,

I posted something similar on the NeuroStars website, but I haven't found any solution yet.

I am trying to download the MNI152NLin2009cAsym templates via template flow. I have tried using the python, but the templateflow-skel.zip file just contained empty nifti files (the non-image files were not empty, though).

I stumbled on this thread (#6) and tried the datalad option for downloading the templates.

I got this error:

[INFO   ] Cloning http://datasets.datalad.org/templateflow/tpl-MNI152NLin2009cAsym [1 other candidates] into '/Users/switt/tpl-MNI152NLin2009cAsym' 
[ERROR  ] Failed to clone from any candidate source URL. Encountered errors per each url were: (OrderedDict([('http://datasets.datalad.org/templateflow/tpl-MNI152NLin2009cAsym', "Cmd('git') failed due to: exit code(128)\n  cmdline: git clone --progress -v http://datasets.datalad.org/templateflow/tpl-MNI152NLin2009cAsym /Users/switt/tpl-MNI152NLin2009cAsym [cmd.py:wait:412]"), ('http://datasets.datalad.org/templateflow/tpl-MNI152NLin2009cAsym/.git', "Cmd('git') failed due to: exit code(128)\n  cmdline: git clone --progress -v http://datasets.datalad.org/templateflow/tpl-MNI152NLin2009cAsym/.git /Users/switt/tpl-MNI152NLin2009cAsym [cmd.py:wait:412]")]),) [install(/Users/switt/tpl-MNI152NLin2009cAsym)] 
install(error): /Users/switt/tpl-MNI152NLin2009cAsym (dataset) [Failed to clone from any candidate source URL. Encountered errors per each url were: (OrderedDict([('http://datasets.datalad.org/templateflow/tpl-MNI152NLin2009cAsym', "Cmd('git') failed due to: exit code(128)\n  cmdline: git clone --progress -v http://datasets.datalad.org/templateflow/tpl-MNI152NLin2009cAsym /Users/switt/tpl-MNI152NLin2009cAsym [cmd.py:wait:412]"), ('http://datasets.datalad.org/templateflow/tpl-MNI152NLin2009cAsym/.git', "Cmd('git') failed due to: exit code(128)\n  cmdline: git clone --progress -v http://datasets.datalad.org/templateflow/tpl-MNI152NLin2009cAsym/.git /Users/switt/tpl-MNI152NLin2009cAsym [cmd.py:wait:412]")]),)]
[WARNING] path not associated with any dataset [get(/Users/switt/tpl-MNI152NLin2009cAsym)] 
action summary:
  get (impossible: 1)
  install (error: 1)

I checked on the datalad website, and it looks as if all of the nifti files have been deleted?

Screen Shot 2019-10-07 at 9 54 00 AM

Is there anyway I can download these templates, or have someone just send me the Harvard Oxford 0thr template in MNI152NLin2009cAsym space? I would really like to finish up some code before the ISMRM deadline.

Thanks,

suzanne

@oesteban oesteban self-assigned this Oct 9, 2019
@amyh101
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amyh101 commented Dec 19, 2019

Hi @oesteban

I am having the same issue with downloading the MNI152NLin2009cAsym templates. I have attempted to download these files using templateflow and directly through GitHub. While the files do download, the nii's are empty.

Any advice?

Thanks!!

@oesteban
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oesteban commented Apr 13, 2020

@amyh101, sorry for the slow response. Did you finally worked this out?

If not, could you check out our documentation first https://www.templateflow.org/ and see whether your particular issue is still missing?

@oesteban
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Okay, I actually started an FAQ with this question - https://www.templateflow.org/client/#why-am-i-getting-zero-sized-nifti-files

Please reopen if you keep having issues.

@oesteban oesteban added the question Further information is requested label Apr 13, 2020
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