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miykael / fmriflows

fmriflows is a consortium of many (dependent) fMRI analysis pipelines, including anatomical and functional pre-processing, univariate 1st and 2nd-level analysis, as well as multivariate pattern analysis.
BSD 3-Clause "New" or "Revised" License
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antsApplyTransforms error in 03_preproc_func part #37

Open zhiliHAN opened 1 year ago

zhiliHAN commented 1 year ago

WARNING message

230209-11:56:53,552 nipype.interface INFO: stderr 2023-02-09T11:56:53.551912:WARNING: In /usr/include/ITK-4.10/itkTransformFactoryBase.h, line 81 230209-11:56:53,554 nipype.interface INFO: stderr 2023-02-09T11:56:53.551912:TransformFactoryBase (0x56294b0c0d70): Refusing to register transform "MatrixOffsetTransformBase_float_3_3" again! Screenshot from 2023-02-09 20-12-19 Screenshot from 2023-02-09 20-13-48

finnally, cuasing the working browser to crash.

Platform details:

running in fmriflows docker,
computer: ubuntu 22.04 LTS

Execution environment

computer: ubuntu 22.04 LTS

Choose one

miykael commented 1 year ago

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.

zhiliHAN commented 1 year ago

Thanks for your reply, I will try as you suggest.

Actually, your project help me a lot for studying fMRI data analysis. Appreciate it.

miykael commented 1 year ago

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!

zhiliHAN commented 1 year ago

It is true and that's why your work really matters, help our rookies to begin.