pydeface can't find template/facemask files

[juan-d]

Hello,

I am trying to run pydeface from a jupyter notebook (Neurodeskapp v 1.14 on a MacBook Pro with M5 chip and macOS Tahoe) but the application cannot find the template and facemask files. Here's how I'm running pydeface:

# install packages
!pip install numpy nibabel nipype pydeface

# import modules
import numpy as np
import nibabel as nib
import nipype

import module
await module.load('fsl/6.0.3')
await module.load('pydeface/2.0.2')

# run pydface
!pydeface /neurodesktop-storage/sub-001_T1w.nii.gz --outfile /neurodesktop-storage/sub-001_T1w_defaced.nii.gz

Here's the error message:

/opt/conda/lib/python3.13/site-packages/pydeface/main.py:6: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
from pkg_resources import require

---

pydeface 2.0.2

---

Temporary files:
/tmp/tmpylyso_1o.mat
/tmp/tmp1vcypyzs.nii.gz
Defacing...
/neurodesktop-storage/sub-001_T1w.nii.gz
260417-07:35:58,914 nipype.interface WARNING:
FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
260417-07:35:59,144 nipype.interface INFO:
stderr 2026-04-17T07:35:59.144954:Image Exception : #63 :: No image files match: /opt/conda/lib/python3.13/site-packages/pydeface/data/mean_reg2mean
260417-07:35:59,146 nipype.interface INFO:
stderr 2026-04-17T07:35:59.146012:Image Exception : #22 :: Failed to read volume /opt/conda/lib/python3.13/site-packages/pydeface/data/mean_reg2mean.nii.gz
260417-07:35:59,146 nipype.interface INFO:
stderr 2026-04-17T07:35:59.146012:Error : No image files match: /opt/conda/lib/python3.13/site-packages/pydeface/data/mean_reg2mean
260417-07:35:59,146 nipype.interface INFO:
stderr 2026-04-17T07:35:59.146148:Failed to read volume /opt/conda/lib/python3.13/site-packages/pydeface/data/mean_reg2mean.nii.gz
260417-07:35:59,146 nipype.interface INFO:
stderr 2026-04-17T07:35:59.146148:Error : No image files match: /opt/conda/lib/python3.13/site-packages/pydeface/data/mean_reg2mean
260417-07:35:59,167 nipype.interface WARNING:
FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
260417-07:35:59,489 nipype.interface INFO:
stderr 2026-04-17T07:35:59.489491:Image Exception : #63 :: No image files match: /opt/conda/lib/python3.13/site-packages/pydeface/data/facemask
260417-07:35:59,490 nipype.interface INFO:
stderr 2026-04-17T07:35:59.490315:Image Exception : #22 :: Failed to read volume /opt/conda/lib/python3.13/site-packages/pydeface/data/facemask.nii.gz
260417-07:35:59,490 nipype.interface INFO:
stderr 2026-04-17T07:35:59.490315:Error : No image files match: /opt/conda/lib/python3.13/site-packages/pydeface/data/facemask
260417-07:35:59,490 nipype.interface INFO:
stderr 2026-04-17T07:35:59.490549:Failed to read volume /opt/conda/lib/python3.13/site-packages/pydeface/data/facemask.nii.gz
260417-07:35:59,490 nipype.interface INFO:
stderr 2026-04-17T07:35:59.490549:Error : No image files match: /opt/conda/lib/python3.13/site-packages/pydeface/data/facemask
Traceback (most recent call last):
File "/opt/conda/bin/pydeface", line 7, in
sys.exit(main())
~~~~^^
File "/opt/conda/lib/python3.13/site-packages/pydeface/main.py", line 95, in main
pdu.deface_image(**vars(args))
~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.13/site-packages/pydeface/utils.py", line 117, in deface_image
warped_mask_img = load(warped_mask)
File "/opt/conda/lib/python3.13/site-packages/nibabel/loadsave.py", line 105, in load
raise ImageFileError(f"Empty file: '{filename}'")
nibabel.filebasedimages.ImageFileError: Empty file: '/tmp/tmp1vcypyzs.nii.gz'

I am able to check that the template file exists:

import os
pydeface_path = os.path.dirname(pydeface.__file__)
template_path = os.path.join(pydeface_path, 'data', 'mean_reg2mean.nii.gz')
print(f"Looking for template at: {template_path}")
print(f"File exists: {os.path.exists(template_path)}")

The above generates the following message:

Looking for template at: /opt/conda/lib/python3.13/site-packages/pydeface/data/mean_reg2mean.nii.gz
File exists: True

Similarly, I am able to list the template file running,

!ls /opt/conda/lib/python3.13/site-packages/pydeface/data/mean_reg2mean.nii.gz

This is the output:

/opt/conda/lib/python3.13/site-packages/pydeface/data/mean_reg2mean.nii.gz

I am also able to load and view the template file with NiiVue:

from ipyniivue import NiiVue
nv = NiiVue()
nv.load_volumes([{"path": "/opt/conda/lib/python3.13/site-packages/pydeface/data/mean_reg2mean.nii.gz"}])
nv

So the template file is there, but pydeface cannot find it.

I appreciate your help with this issue.

[stebo85]

It looks like you have a collision of PyDeface versions:

You install the python version of PyDeface:

!pip install numpy nibabel nipype pydeface

and then you load the container version of PyDeface on top:

await module.load('pydeface/2.0.2')

I have a look if this is causing the problem - but it most likely would do what you describe.

my recommendation is to remove the python installs completely:
!pip install numpy nibabel nipype pydeface

[stebo85]

Dear @juan-d - I reproduced your problem and confirm the fix:

1. Installing pydeface as a python package breaks the python installation because it's so old that it interferes with setup tools - don't do that :)

2. Just load pydeface from Neurodesk and run it:

import module
await module.load('pydeface/2.0.2')

# run pydface
!pydeface /neurodesktop-storage/sub-001_T1w.nii --outfile /neurodesktop-storage/sub-001_T1w_defaced.nii

[juan-d]

@stebo85

Thanks a lot for that. That worked! I thought I had done that (in an earlier try) but obviously I must have done something different.