Outputs

PARS stores generated files inside the processed subject folder.

Image-processing output

data/subjects/{subject_name}/pre_model.nii.gz

This is the labelled geometry passed from 01_ImageProcess.ipynb to 02_MeshCreation.ipynb.

Temporary registration and segmentation files are also created under folders such as:

data/subjects/{subject_name}/tmp/
data/subjects/{subject_name}/img/fast/
data/subjects/{subject_name}/img/bet/

These files are useful for checking intermediate processing but are not the final mesh.

Mesh outputs

By default, mesh files are written to:

data/subjects/{subject_name}/output/

The main files are:

File	Description
mesh.k	initial mesh generated from the labelled volume
mesh_smoothed.k	mesh after surface smoothing
mesh_smoothed_revised.k	final mesh after brain-skull contact repair

For normal downstream use, inspect and use mesh_smoothed_revised.k.

The output folder may also contain supporting keyword, set or intermediate files generated by the mesh-creation code. Keep these files with the model unless the downstream simulation workflow explicitly requires a smaller subset.