8000 Issues with dipy_align_syn · Issue #2648 · dipy/dipy · GitHub
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Issues with dipy_align_syn #2648

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Closed
6 tasks
Tracked by #2761
, #2911
...
pjsjongsung opened this issue Sep 22, 2022 · 4 comments
Closed
6 tasks
Tracked by #2761
, #2911
...

Issues with dipy_align_syn #2648

pjsjongsung opened this issue Sep 22, 2022 · 4 comments
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type:Bug Fix

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@pjsjongsung
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Description

I have been following the tutorial for dipy_align_syn, and it seems that the --out_inv_static option in dipy_align_syn does not work and the inverse transformed static image is not saved.

Also, I spent a lot of time figuring out that without the --force option, if there is already a file with the output image's name, the command terminates without any information. I think it would be nice if it at least printed a warning/error that one should use the --force option if they want to overwrite.

I think these are just minor issues and can be resolved with some small fixes, but is important since it is related to how convenient the method is to use.

Way to reproduce

  • Code example
    dipy_align_syn moving.nii.gz static.nii.gz --force --metric "cc" --out_dir "syn_reg_output" --out_warped "warped.nii.gz" --out_inv_static "inv.nii.gz" --out_field "field.nii.gz"
  • Relevant images (if any)
  • Operating system and version (run python -c "import platform; print(platform.platform())")
    Windows-10-10.0.19043-SP0
  • Python version (run python -c "import sys; print("Python", sys.version)")
    Python 3.8.12
  • dipy version (run python -c "import dipy; print(dipy.__version__)")
    1.5.0
  • dependency version (numpy, scipy, nibabel, h5py, cvxpy, fury)
    • import numpy; print("NumPy", numpy.version)
      1.22.4
    • import scipy; print("SciPy", scipy.version)
      1.8.0
    • import nibabel; print("Nibabel", nibabel.version)
      3.2.2
    • import h5py; print("H5py", h5py.version)
      3.6.0
    • import cvxpy; print("Cvxpy", cvxpy.version)
      1.2.1
    • import fury; print("fury", fury.version)
      0.8.0
@skoudoro
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Thank you for the feedback @pjsjongsung,

we will look into it

lb-97 added a commit to lb-97/dipy that referenced this issue Feb 26, 2023
@lb-97
Update SynRegistrationFlow for dipy#2648
aac1b63 
Updated the class to save inverse transformed static image
@lb-97
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lb-97 commented Feb 26, 2023

@skoudoro, I had made a commit for this issue and raised a pull request. Kindly review and let me know what you think.

skoudoro added a commit that referenced this issue Mar 6, 2023
@skoudoro
Merge pull request #2733 from lb-97/master
bb116d5 
Update SynRegistrationFlow for #2648
@skoudoro skoudoro mentioned this issue Mar 27, 2023
Merged
33 tasks
@skoudoro skoudoro mentioned this issue Sep 26, 2023
Merged
41 tasks
@skoudoro
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skoudoro commented Oct 4, 2023

Can I close this issue @pjsjongsung? it seems it has been fixed by #2733.

Please, try and keep us updated. Thanks !

@pjsjongsung
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I think we can. Thank you @lb-97 @skoudoro !

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