Comments (4)
Thank you @zhiliHAN for this pointer. It's true, the ANTS version inside the docker container is from 2017 and the container itself was finalized in 2019. Updating all packages and dependencies to Python 3.9 and ubuntu 22.04 unfortunately isn't necessairly straightforward - especially as some Python packages fmriflows
uses changed dramatically (e.g. pybids
and nistats
).
At this point in time, I unfortunately don't have the time to investigate this further or upgrade the packages to newest package versions. But if you're interested then you could give it a try here: https://github.com/miykael/fmriflows/blob/master/generate.sh
Once the file is updated, you can just run bash generate.sh
to get the new Dockerfile and follow this with sudo docker build -t fmriflows .
to create the container. And once all of this is built, using docker run -it --rm fmriflows python /home/neuro/test_notebooks.py
can be run to test if the test notebooks are still passing.
from fmriflows.
Thanks for your reply, I will try as you suggest.
Actually, your project help me a lot for studying fMRI data analysis. Appreciate it.
from fmriflows.
Thanks for the nice feedback! I'm happy that it helps and it's unfortunate that I can't help you more with this issue, but it's a very quickly changing/advancing field - which is great as it provides new tools but also difficult because things quickly become obsolete or different. Good luck!
from fmriflows.
It is true and that's why your work really matters, help our rookies to begin.
from fmriflows.
Related Issues (19)
- summary html [enh] HOT 4
- Should there be an option to shorten normalization time? HOT 3
- How to do group analysis with SpaceNet? HOT 1
- How to do group analysis with Searchlight?
- Filters in functional preprocessing should be orthogonal HOT 3
- High-Pass value in CompCor estimation HOT 1
- Report of functional preprocessing doesn't plot individual runs, only the first one HOT 1
- Anatomical Pipeline: Segmentation output should be compressed HOT 4
- Error running workflow in 01_preproc_anat HOT 4
- html reports dependency
- Creation of `00_parameter_specification.ipynb` notebook
- Descriptive text in notebooks needs to be updated to publication HOT 1
- Error after pulling HOT 2
- 06_analysis_multivariate “ImportError: cannot import name analyze” HOT 4
- Fail to use docker HOT 1
- proposals for fmriflows logo HOT 29
- Workflow and node sub-segmentation HOT 1
- Rewriting of Function Nodes, concerning file paths.
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from fmriflows.