MRI2circ

Build docker

docker build -t mri2circ -f Dockerfile .

Inputs

T1 image (nifti) Age in years (float): Template ranges 0-2,3-7,8-13,14-35 --neonatal: optional, if present Age should be entered in weeks as an integer value ranging from 36-44

Run docker

1. img_path (optional, default: "/data/input.nii.gz"): Path to the MRI image file
2. age (optional, default: 35): Age of the subject
3. output_path (optional, default: "/data/output"): Path to the output folder

Optional named arguments:

• --neonatal: Flag to indicate if the subject is neonatal
• --theta_x THETA_X (default: 0): Rotation angle around x-axis
• --theta_y THETA_Y (default: 0): Rotation angle around y-axis
• --theta_z THETA_Z (default: 0): Rotation angle around z-axis
• --conductance_parameter CONDUCTANCE_PARAMETER (default: 3.0): Conductance parameter for anisotropic diffusion
• --smoothing_iterations SMOOTHING_ITERATIONS (default: 5): Number of smoothing iterations
• --time_step TIME_STEP (default: 0.0625): Time step for anisotropic diffusion
• --threshold_filter {Otsu,Binary} (default: "Otsu"): Threshold filter method
• --mip_slices MIP_SLICES (default: 5): Number of slices for maximum intensity projection

minimal docker run: docker run -v /home/philip-mattisson/Desktop/data:/data
mri2circ
python3.9 /executables/new_process_image_with_options.py
/data/sub-pixar066_anat_sub-pixar066_T1w.nii.gz 35 /data/V2Out

all arguments

docker run -v /home/philip-mattisson/Desktop/data:/data
mri2circ
python3.9 /executables/new_process_image_with_options.py
/data/sub-pixar066_anat_sub-pixar066_T1w.nii.gz
35
/data/V2Out
--neonatal
--theta_x 10
--theta_y 5
--theta_z 15
--conductance_parameter 2.5
--smoothing_iterations 7
--time_step 0.05
--threshold_filter Otsu
--mip_slices 3

References

Automated temporalis muscle quantification and growth charts for children through adulthood doi.org/10.1038/s41467-023-42501-1