Avnirpy

Avnirpy is a library developed by Avnir Lab under the direction of Dr. Letourneau Guillon. It includes a range of tools primarily designed for CT scans segmentation and analysis.

Prerequisites

Before installing Avnirpy, ensure you have the following prerequisites:

Python >= 3.9 and < 3.12 installed on your system. You can check your Python version by running:
python3 --version
Git installed on your system. If not installed, you can install Git using the following commands:
sudo apt update sudo apt install git

We highly recommend using a virtual environment to manage your Python dependencies. You can create a virtual environment by following the Python documentation.

Installation

You can install Avnirpy by cloning the repository and using pip. Run the following command to install Avnirpy:

git clone git@github.com:llgneuroresearch/avnirpy.git
cd avnirpy
pip install -e .

To test your installation, you can run the following command:

avnir_print_header.py -h

Example

Here is an example command to run Avnirpy script:

# Create input and output directories
ls input_data/
    image1.nii.gz

# Run Avnirpy
python avnir_print_header.py input_data/image1.nii.gz

# Command line output
<class 'nibabel.nifti1.Nifti1Header'> object, endian='<'
sizeof_hdr      : 348
data_type       : b''
db_name         : b''
extents         : 0
session_error   : 0
regular         : b''
dim_info        : 0
dim             : [  3 512 512  34   1   1   1   1]
intent_p1       : 0.0
intent_p2       : 0.0
intent_p3       : 0.0
intent_code     : none
datatype        : float32
bitpix          : 32
slice_start     : 0
pixdim          : [1.       0.488281 0.488281 5.373771 1.       1.       1.       1.      ]
vox_offset      : 0.0
scl_slope       : nan
scl_inter       : nan
slice_end       : 0
slice_code      : unknown
xyzt_units      : 2
cal_max         : 0.0
cal_min         : 0.0
slice_duration  : 0.0
toffset         : 0.0
glmax           : 0
glmin           : 0
descrip         : b''
aux_file        : b''
qform_code      : unknown
sform_code      : aligned
quatern_b       : 0.0
quatern_c       : -0.18652385
quatern_d       : 0.9824504
qoffset_x       : 125.0
qoffset_y       : 139.38208
qoffset_z       : -7.3461156
srow_x          : [ -0.488281   0.         0.       125.      ]
srow_y          : [  0.         -0.4543053  -1.969492  139.38208  ]
srow_z          : [ 0.         -0.17895542  4.999852   -7.3461156 ]
intent_name     : b''
magic           : b'n+1'

Every scripts available are in the avnirpy/scripts directory. They all begin with avnir_. If you want to know more about the scripts, you can run the script with the -h option.