[ENH]: Memory issue during layer creation

[marcobarilari]

Is there an existing issue for this?

• I have searched the existing issues

New feature

With upsampled data, the layering of one subject is "killed" after cruise step of first hemisphere due to memory (RAM) issue. Working with a computer with 64GB of RAM.

Not sure but I suspect that the problem is that the code keeps the output of the below functions dave in the output variable hogging the memory.

cortex = nighres.brain.extract_brain_region(
   segmentation=segmentation_img[0],
   levelset_boundary=levelset_boundary_img[0],
   maximum_membership=max_membership_img[0],
   maximum_label=max_label_img[0],
   extracted_region=roi,
   save_data=True,
   file_name=f"{output_filename}_hemi-{label}",
   output_dir=output_dir,
)

cruise = nighres.cortex.cruise_cortex_extraction(
   init_image=cortex["inside_mask"],
   wm_image=cortex["inside_proba"],
   gm_image=cortex["region_proba"],
   csf_image=cortex["background_proba"],
   normalize_probabilities=True,
   save_data=True,
   file_name=f"{output_filename}_hemi-{label}",
   output_dir=output_dir,
)

My possible solution, if this is the problem, would be to refactor the code and after eg the first step `cortex = nighres.brain.extract_brain_region` clear `cortex` and make `cruise = nighres.cortex.cruise_cortex_extraction` load the nii saved output of the previous step.

Though, the saved files from these two steps do not wait more than ~4GB

Unclear documentation

No response