AtlasPack 'get' failing

Software Support
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Summary of what happened:

Hi! I have been trying to clone AtlasPack using datalad in order to access the tpl-MNI152NLin6Asym_atlas-4S456Parcels_res-01_dseg.nii file. While I can clone the dataset successfully using DataLad, when I try to ‘get’ the file I get the below error. I’m using a remote system but have previously been able to clone and ‘get’ other files without issues. Thanks for any insight into how to debug this!

Command used (and if a helper script was used, a link to the helper script or the command generated):

datalad get tpl-MNI152NLin6Asym_atlas-4S456Parcels_*

Error message:

get(error): tpl-MNI152NLin6Asym_atlas-4S456Parcels_res-01_dseg.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)]
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Hi @lucinda,

Can you try downloading the atlaspack docker/singularity image (pennlinc/atlaspack:0.1.0) and copying the files from there? The files should be in /AtlasPack in the container.

Best,
Steven

3

@tsalo is this the same error you’re seeing with your openneuro datalad gets? I wonder if there’s something going on with git annex

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4

Hi Steven! Thanks so much for your quick reply. Not sure if I’m missing something, but after pulling the docker image for AtlasPack 0.1.0 and saving it into a .tar file, I’m not seeing an /AtlasPack folder, just one called /blobs. There don’t seem to be any atlas files that I can see. Thanks so much again for any insight!

5

Hi @lucinda,

Enter the container with singularity shell -e -B $PATH_YOU_WANT_TO_WRITE_TO $IMG and then you should be able to copy from /AtlasPack to $PATH_YOU_WANT_TO_WRITE_TO with cp /AtlasPack/$FILE_YOU_WANT_TO_COPY $PATH_YOU_WANT_TO_WRITE_TO/.

Best,
Steven

6

Hi @Steven,

Thank you for these steps! I tried that earlier but get a fatal error that “/bin/sh does not exist in container”. So strange–I just tried rebuilding the container and don’t get any errors there. Thanks again for your thoughts!

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Hi @lucinda,
What about with

singularity exec --bind $PWD:/host-dir /path/to/your/container.sif cp /AtlasPack/tpl-MNI152NLin6Asym_atlas-4S456Parcels_res-01_dseg.nii.gz /host-dir/

and if that doesn’t work try adding --shell /bin/bash in the exec arguments.

Best,
Steven

8

Hi @Steven! Thank you so much. Tried these but unfortunately got the following errors:

singularity exec --bind $PWD:/host-dir /path/to/your/container.sif cp /AtlasPack/tpl-MNI152NLin6Asym_atlas-4S456Parcels_res-01_dseg.nii.gz /host-dir/

FATAL:   "cp": executable file not found in $PATH

Adding --shell /bin/bash gave me an unrecognized argument error

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The atlaspack image doesn’t have an os in it, it’s empty except for the atlaspack files. We only use that image for copying them into other images - I’m not sure how to get files out of them outside of a docker build

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@mattcieslak ah, makes sense. Thank you for that info!

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Hi @lucinda,

Sending to you now, but I was able to get the atlases by entering the qsirecon singularity shell and copying them to a local a directory within, just in case other readers encounter this error.

Best,
Steven

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