templates download as empty nifti files

[switt4]

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?

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

[amyh101]

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]

@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]

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.

[NatashaLTaylor]

Hi,
I am having a similar but slightly different problem specifically with downloading relevant files for tpl-MNI152NLin2009bSym and tpl-MNI152NLin2009bAsym.
Code as follows through python:
from templateflow import api as tflow path = tflow.get("MNI152NLin2009bSym", desc=None, resolution=1, suffix="T1w", extension="nii.gz") print(path)
These files are only 353 bytes - and I cannot use them in any other functions, specifically trying to use these as a template for a reference in flirt.
Receive the following error message:
Image Exception : #22 :: Failed to read volume tpl-MNI152NLin2009bSym_res-1_T1w.nii.gz
Error : Error: file does not appear to be a valid NIFTI or ANALYZE image

I suspect for some reason the tpl-MNI152NLin2009bSym folder is not properly downloading through templateflow - I've confirmed the other resolutions have downloaded correctly such as tpl-MNI152NLin2009aSym.
Any assistance on this would be greatly appreciated - I'm sure I've just missed something.

Thanks!
Natasha