edanif 0.1.7

EDA-NIf creates a dataframe containing meta information of NIfTi files and provides several useful features.

EDA-NIf (EDA NIfTI)

Tool for Exploratory Data Analysis of Neuroimaging Informatics Technology Initiative(NIfTI) format
EDA-NIf creates a dataframe containing meta information of NIfTi file format and provides several useful functions.

Installation

pip install edanif

Beta versions with official documentation are provided starting from major version 1.

Tutorial

We provide tutorial notebooks for all the features we offer. We plan to provide additional docstrings or documentation from the official distribution version (major version 1 or higher).

1. Main-tutorials: https://github.com/DSDanielPark/EDA-NIf/blob/main/tutorials/edanif_tutorial.ipynb
2. Sub-tutorial-folder: https://github.com/DSDanielPark/EDA-NIf/tree/main/tutorials

Main Feature

See sample data folder tree...

The sample data folder is designed with an unnecessary and complex structure to show that all nifti files under the top-level folder path are collected recursively. If you are using the BIDS format, you only need to insert keywords properly.

Example folder tree

edanif.eda_nif.meta_df

If you enter only the top-level folder containing nifti files, you can get a data frame for all nifti files.

1. In case of raw nifti files

   import edanif
   
   raw_nifti_folder= '../data/raw_nifti'
   df_raw_nii = edanif.meta_df(raw_nifti_folder, 'nii.gz', 'df_raw_nii_meta.csv', False)
   

   result dataframe: https://github.com/DSDanielPark/EDA-NIf/blob/main/tutorials/result/df_raw_nii_meta.csv

2. In case of mask nifti files (binary files only)

   import edanif
   
   mask_nifti_folder= '../data/mask_nifti'
   df_mask_nii = edanif.meta_df(mask_nifti_folder, 'mask.nii.gz', 'df_mask_nii_meta.csv', True)
   

   result dataframe: https://github.com/DSDanielPark/EDA-NIf/blob/main/tutorials/result/df_mask_nii_meta.csv

Features

1. edanif.eda_nif
   1.1 count_center_voxel_labels
   1.2 meta_df: enter only the top-level folder containing nifti files, you can get a data frame for all nifti files.
   

2. edanif.vis_nif
   2.1 save_nifti_images
   

3. edanif.utils.util
   3.1 find_all_files
   3.2 save_print_instance
   

4. edanif.process.preprocess
   4.1 count_center_voxel_labels
   4.2 if_minus_return_0
   4.3 get_nonzero3d
   4.4 get_nonzero3d_shape
   4.5 get_hardcrop
   4.6 threshold_at_two
   4.7 monai_cropforeground
   4.8 get_nonzero_xyz_of_nii
   

5. edanif.process.registration
   5.1 RegistrationMetric
   

6. edanif.process.resampling
   6.1 make_isotropic
   6.2 resample_fixedsize_fixedspacing
   6.3 resampling
   

7. edanif.process.trans_morph
   7.1 voxel_erosion
   7.2 voxel_dilation
   7.3 get_boundary_diff_index
   

• Feature development and unit testing are ongoing. We will update it whenever time permits.

References

[1] NiBabel https://nipy.org/nibabel/
[2] SimpleITK https://simpleitk.org/
[3] MONAI https://monai.io/
[4] AntsPy https://github.com/ANTsX/ANTsPy

Contacts

Maintainer: Daniel Park, South Korea e-mail [e-mail]