miykael/gif_your_nifti

How to create fancy GIFs from an MRI brain image

Hi there 👋

I'm Michael, a senior machine learning researcher & neuroscientist fascinated by hidden patterns in the digital world. My curiosity and expertise extend across neuroimaging, computer vision, vital signs, AR/VR, and multi-sensor sensing. With a strong background in signal processing, open source, and Python, I explore these domains with an open and innovative mindset.

Eager to push boundaries and think outside the box, I welcome opportunities to craft unique solutions and collaborate on new projects. Don't hesitate to contact me!

For more about me, check out my personal page under: https://miykael.github.io/

gif_your_nifti's Issues

Add overlay?

Might it be possible to visualize two images, anatomical base with an overlay with a different color scheme?

Output Gif is stretched horizontally and top + bottom are covered in plain grey

I am not sure what causes this but i've used 2 different datasets and sometimes it outputs this format where the Gif looks stretched and the top and bottom are just covered by grey.

Please let me know if there is any fix to this, thanks!

Error

Hi !
hope you are fine . Can u help me in solving ths problem

gif_your_nifti '/home/abir/Bureau/data/training/patient028/patient028_4d.nii'
Traceback (most recent call last):
  File "/usr/local/bin/gif_your_nifti", line 11, in <module>
    load_entry_point('gif-your-nifti==0.2.0', 'console_scripts', 'gif_your_nifti')()
  File "/home/abir/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 489, in load_entry_point
    return get_distribution(dist).load_entry_point(group, name)
  File "/home/abir/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2852, in load_entry_point
    return ep.load()
  File "/home/abir/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2443, in load
    return self.resolve()
  File "/home/abir/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2449, in resolve
    module = __import__(self.module_name, fromlist=['__name__'], level=0)
  File "build/bdist.linux-x86_64/egg/gif_your_nifti/__main__.py", line 5, in <module>
  File "build/bdist.linux-x86_64/egg/gif_your_nifti/core.py", line 4, in <module>
  File "/usr/local/lib/python2.7/dist-packages/nibabel-3.1.0-py2.7.egg/nibabel/__init__.py", line 40, in <module>
    from . import analyze as ana
  File "/usr/local/lib/python2.7/dist-packages/nibabel-3.1.0-py2.7.egg/nibabel/analyze.py", line 935
    def from_file_map(klass, file_map, *, mmap=True, keep_file_open=None):
                                        ^
SyntaxError: invalid syntax

RuntimeError: Python is not installed as a framework

I use MacOS (El Capitan) and Conda
Looks like there is a MacOS related issue in the installation.
After I install the package I got this error:
RuntimeError: Python is not installed as a framework. The Mac OS X backend will not be able to function correctly if Python is not installed as a framework. See the Python documentation for more information on installing Python as a framework on Mac OS X. Please either reinstall Python as a framework, or try one of the other backends. If you are using (Ana)Conda please install python.app and replace the use of 'python' with 'pythonw'. See 'Working with Matplotlib on OSX' in the Matplotlib FAQ for more information.

After googling it I found this solution on a Stackoverflow page:[https://stackoverflow.com/questions/21784641/installation-issue-with-matplotlib-python]

I assume you have installed the pip matplotlib, there is a directory in you root called ~/.matplotlib.
Create a file ~/.matplotlib/matplotlibrc there and add the following code: backend: TkAgg

After doing this now it works and I can create gifs of my nifti. Hooray!!!

Encountering errors when installing and running command

Hi there, I'm not sure if this is the right place to ask questions, but I have been having some trouble getting "gif_your_nifti" to work and was wondering if this was the correct place to get some help?

Allow for recent imageio

• #12

was addressed via pinning of imageio in

• #13

but that now causes

ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
gif-your-nifti 0.2.1 requires imageio<2.28, but you have imageio 2.34.1 which is incompatible.
Successfully installed argparse-1.4.0 bidsonym-0.0.6+17.g8417c18.dirty citeproc-py-0.6.0 duecredit-0.10.2 imageio-2.34.1 nilearn-0.10.4 scikit-learn-1.5.0 threadpoolctl-3.5.0
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv
Removing intermediate container 6706dd6d886d

while installing bidsonym

• PeerHerholz/BIDSonym#81

Ideally issue should be properly resolved by adjusting used interface and removing (or at least raising to < 2.35 upper bound on imageio)

Bug: incompatible with `imageio` verison 2.28

imageio version 2.28 comes with imageio/imageio#871 which finally came into effect in imageio/imageio#824 no longer works with git_your_nifti:

> gif_your_nifti data/brats2020-training-validation-data/BraTS2020_TrainingData/MICCAI_BraTS2020_TrainingData/BraTS20_Training_354/BraTS20_Training_354_seg.nii
====================
gif_your_nifti 0.2.0
====================
Selections:
  mode = normal
  size = 1
  fps  = 20
Traceback (most recent call last):
  File "/path/to/venv/bin/gif_your_nifti", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/path/to/venv/lib/python3.11/site-packages/gif_your_nifti/__main__.py", line 60, in main
    core.write_gif_normal(f, cfg.size, cfg.fps)
  File "/path/to/venv/lib/python3.11/site-packages/gif_your_nifti/core.py", line 192, in write_gif_normal
    mimwrite(filename.replace(ext, '.gif'), new_img,
  File "/path/to/venv/lib/python3.11/site-packages/imageio/v2.py", line 484, in mimwrite
    return file.write(ims, is_batch=True, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/path/to/venv/lib/python3.11/site-packages/imageio/plugins/pillow.py", line 354, in write
    raise TypeError(
TypeError: The keyword `fps` is no longer supported. Use `duration`(in ms) instead, e.g. `fps=50` == `duration=20` (1000 * 1/50).

Here is the dataset being used.

The version should be pinned in setup.py for those installing like so:

pip install git+https://github.com/miykael/gif_your_nifti.git

Request: `setup.py` pulling requirements from `requirements.txt`

setuptools>=62.6 supports install_requires coming from a requirements.txt.

It would be good to sync up requirements.txt with setup.py's install_requires using this.