Issue with pydeface on linux VM

1

Hi all,

We’re running into issues de-facing anatomical files on our lab’s linux VM. Please note that this issue does not arise when running pydeface on a mac. Here’s the error we get when running pydeface:

Defacing…
sub-014_ses-1_T1w.nii.gz
Traceback (most recent call last):
File “/PathLocalToMyComputer/anaconda3/bin/pydeface”, line 8, in
sys.exit(main())
File “/PathLocalToMyComputer/anaconda3/lib/python3.9/site-packages/pydeface/main.py”, line 95, in main
pdu.deface_image(**vars(args))
File “/PathLocalToMyComputer/anaconda3/lib/python3.9/site-packages/pydeface/utils.py”, line 124, in deface_image
masked_brain = Nifti1Image(outdata, infile_img.get_affine(),
File “/PathLocalToMyComputer/anaconda3/lib/python3.9/site-packages/nibabel/deprecator.py”, line 181, in deprecated_func
raise error_class(message)
nibabel.deprecator.ExpiredDeprecationError: get_affine method is deprecated.
Please use the img.affine property instead.

  • deprecated from version: 2.1
  • Raises <class ‘nibabel.deprecator.ExpiredDeprecationError’> as of version: 4.0

Has anyone encountered a similar issue?

Thanks,
Frank

2

Hello,

Can you try making sure that pydeface dependencies are at the tested versions?
image

Or try the docker container: Docker Hub

Best,
Steven

3

Hi Steven,

Thanks for providing details. It’s strange because I’ve got those programs installed within my conda environment. Here’s my yaml file I use to create the environment.

channels:

  • conda-forge
    dependencies:
  • pip
  • dcm2niix
  • dcm2bids
  • joblib
  • nibabel
  • numpy
  • pandas
  • nipype
  • python>=3.7
  • scipy
  • fslpy
  • pip:
    • bidsify
    • cmake
    • fmriprep-docker
    • bids-validator
    • pydeface

I’m still getting the issue “nibabel.deprecator.ExpiredDeprecationError: get_affine method is deprecated.
Please use the img.affine property instead.”

Anything seem out of the ordinary from your point of view?

Thanks again,
FG

4

Are these packages at those specific versions?

5

Great question! I checked this by ensuring that the versions I downloaded were set to the tested version.

name: garcealabvm_pydeface_py37_env
channels:

  • conda-forge
    dependencies:
  • pip
  • dcm2niix
  • dcm2bids
  • joblib
  • nibabel==2.5.1
  • numpy==1.17.1
  • pandas
  • nipype==1.3.0
  • python>=3.7
  • scipy
  • fslpy
  • pip:
    • jq
    • bidsify
    • cmake
    • fmriprep-docker
    • bids-validator
    • pydeface

When I did that I couldn’t not get pydeface to run. It crashed immediately (here’s the log file: Dropbox - PydefaceLog.rtf - Simplify your life)).

This was very different than my experience described above. In that case, pydeface will run for about 5 mins to run before it throws me the “img.affine” issue (described above). I’m not sure what’s going on.

FG

6

Hmm, sounds frustrating :confused: can you try using the docker container?

7

Hey Steven,

There is now a new version of pydeface (2.0.2) that addresses the issue I documented above. After updating pydeface the issue went away!

Thanks again for your input.

FG

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