Preprocessing

Available tools

Fetpype pre-processes the data in the following order.

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Data Loading (→ Brain extraction) → Resolution checks → Cropping → Denoising → Bias field correction → Output checks

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The three steps in boldface are run from a container.

Note

All the container runs use the command below and are passed through the function run_prepro_cmd

Config structure

The config file is structured as follows:

brain_extraction:
  docker:
    cmd: "docker run --gpus all <mount> thsanchez/fetpype_utils:latest run_brain_extraction 
      --input_stacks <input_stacks> 
      --output_masks <output_masks> 
      --method fet_bet"
  singularity:
    cmd: "singularity run --bind <singularity_mount> --nv
      <singularity_path>/fetpype_utils.sif
      run_brain_extraction
      --input_stacks <input_stacks> 
      --output_masks <output_masks> --method monaifbs"

check_stacks_and_masks:
  enabled: true

denoising:
  enabled: true
  docker:
    cmd: "docker run <mount> thsanchez/fetpype_utils:latest run_denoising 
      --input_stacks <input_stacks> 
      --output_stacks <output_stacks>"
  singularity:
    cmd: "singularity run --bind <singularity_mount>
      <singularity_path>/fetpype_utils.sif
      run_denoising
      --input_stacks <input_stacks> 
      --output_stacks <output_stacks>"
cropping:
  enabled: true

bias_correction:
  enabled: true
  docker:
    cmd: "docker run <mount> thsanchez/fetpype_utils:latest run_bias_field_correction 
      --input_stacks <input_stacks> 
      --input_masks <input_masks> 
      --output_stacks <output_stacks>"
  singularity:
    cmd: "singularity run --bind <singularity_mount>
      <singularity_path>/fetpype_utils.sif
      run_bias_field_correction
      --input_stacks <input_stacks> 
      --input_masks <input_masks> 
      --output_stacks <output_stacks>"

Note

• Each pre-processing step that can be disabled has a boolean entry enabled: true that can be set to false.
• The steps that rely on a container are set with a list of valid tags

Tags

There are a limited set of tags that can be used for preprocessing:

Command	Description	Comments
<mount>	Where the different folders will be mounted on Docker	Docker only
<singularity_mount>	Where the different folders will be mounted on Singularity	Singularity only
<singularity_path>	The base path of the Singularity image	Singularity only
<input_stacks>	The list of inputs stacks will be given as arguments	Mutually exclusive with <input_dir>
<input_masks>	The list of inputs masks will be given as arguments	Mutually exclusive with <input_masks_dir>
<output_stacks>	The list of output stacks
<output_masks>	The list of output masks