introduction_dataset doesn't get anatomical used by introduction_quickstart

[Shotgunosine]

It looks like the introduction_quickstart notebook is referring to an anatomical that isn't downloaded by datalad in the introduction_dataset notebook. I've submitted a short pr to download the anatomicals.

[miykael]

@Shotgunosine - Thank you for investigating this.
But I've tried to run it on the current docker image and it seems to have worked. Are we talking about /data/ds000114/sub-01/ses-test/anat/sub-01_ses-test_T1w.nii.gz? In theory this file should be included in the docker image, as it's downloaded here with datalad get -r sub-01/ses-test/anat sub-01/ses-test/func/*fingerfootlips*.

Could you please open your docker image with the bash command at the end:

docker run -it --rm miykael/nipype_tutorial bash

And run the following command:

ls -ll /neurodocker/neurodocker_specs.json

Is the date of your file also the 13th of September?

-rw-r--r-- 1 neuro root 4058 Sep 13 13:17 /neurodocker/neurodocker_specs.json

[Shotgunosine]

Sorry for leaving out an important detail, I was mounting in my own data directory as described in the docker introduction:
docker run -it --rm -v /path/to/nipype_tutorial/:/home/neuro/nipype_tutorial -v /path/to/data/:/data -v /path/to/output/:/output -p 8888:8888 miykael/nipype_tutorial jupyter notebook

If you've done that, then you run the bids & tutorial dataset notebook, then you try to run any of the quickstarts, you find that you don't have the anats.

[miykael]

Ah, now I see. Yes, that's true. This is because -v /path/to/data/:/data will overwrite any tutorial data from the docker image with your own dataset. In this case, you're right with your commit.

To reduce download time on circleci, could you restrict the download to just subject 1, i.e. change your line to /data/ds000114/sub-01/ses-test/anat/*? This should be enough for the tutorials otherwise, no?

[Shotgunosine]

I’ll do that

…

Sent from my iPhone

On Oct 2, 2018, at 6:02 PM, Michael Notter ***@***.***> wrote: Ah, now I see. Yes, that's true. This is because -v /path/to/data/:/data will overwrite any tutorial data from the docker image with your own dataset. In this case, you're right with your commit. To reduce download time on circleci, could you restrict the download to just subject 1, i.e. change your line to /data/ds000114/sub-01/ses-test/anat/*? This should be enough for the tutorials otherwise, no? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.