I just realized that I used the dock-pull to get the fmriprep docker image, it explains why I can’t use fmriprep-docker .
To run the fmriprep-docker wrapper, do I need to first delete the current fmriprep docker image? i.e., should I remove my current version of fmriprep and then use pip install --user --upgrade fmriprep-docker, or I can directly install without deleting the current docker image? (Assuming that the free space on my current drive is not that much).
This might be a deeper problem. You can try pip install --user --upgrade pip, but I have a suspicion that it’s just broken. There may be a better solution, but at that point, I would personally just delete my ~/.local directory and start from scratch.
I really just meant rm -r $HOME/.local. But note that that’s pretty drastic, and will remove a lot of things you have installed. If you’re content to reinstall things as you need them, then it should be fine. But you might be able to try something a little more confined like:
here are my docker images
hcp4715@hcp4715-Precision-5510:~$ sudo docker images
REPOSITORY TAG IMAGE ID CREATED SIZE
nipy/heudiconv latest ee62aa995a80 3 weeks ago 1.27GB
poldracklab/fmriprep latest d4b288343142 4 weeks ago 11.6GB
hello-world latest fce289e99eb9 8 weeks ago 1.84kB
I will try to figure out the environment (s) first, seems a bit complicated. I only knew that conda can be used to set different environment, didn’t expect docker also related to env.
Mar 10th, 2019 update:
Finally, I could run fmriprep-docker.
I figured out that I set the python 3.6 from anaconda as my default, instead of directly installed by command from terminal. That caused the permission problem of pip upgrade problem. I solved it by modifying the permission of anaconda.