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Parkinson's pipeline

Table of Contents

Prerequisities

The Parkinson's Pipeline has the following software requirements:

  1. A 64-bit Linux Operating System.

  2. Advanced Normalisation Tools (https://github.com/ANTsX/ANTs) for N4 bias field correction.

  3. ROBEX brain extraction tool (https://www.nitrc.org/projects/robex).

  4. Medical Image Registration ToolKit (https://github.com/BioMedIA/MIRTK).

  5. MATLAB (we have tested version R2018a, but later versions and some older versions should work as well).

Setup

Data

The T1-weighted and neuromelanin-sentitive Nifti data to be processed must be located in a specific folder named Original inside ${GITHUB_ROOT}, where ${GITHUB_ROOT} refers to the folder where this repository has been cloned into. It must also adhere to the following naming convention:

${GITHUB_ROOT}
   |
   ---- Original
           |
           ---- sub-${subject_id}-${timepoint}_T1w.nii.gz
           ---- sub-${subject_id}-${timepoint}_${nm_seq_type}.nii.gz
  • ${subject_id} is a unique identifier for each subject that can have any format.
  • ${timepoint} is the timepoint of the data (for longitudinal studies) and must be a single digit integer, typically starting from "1" for baseline data then "2" for first follow-up, and so on. If no longitudinal data is used, this can be any single digit integer from "1" onwards.
  • ${nm_seq_type} is the name of the neuromelanin-sensitive sequence this data represent and can have any format but must be setup as a sequence type (see Neuromelanin-sensitive sequence names).

Environmental variables

The script SetUpVariables.sh serves as a way for the user to setup the paths of the main software pre-requisites the pipeline has. Therefore, for the pipeline to work, the user has to edit this file to specify the specific software paths on their environment.

Neuromelanin-sensitive sequence names

The script SetUpNMTypes.sh serves as a way for the user to setup the names of the neuromelanin-sensitive sequences that will be processed. The user has to edit this file to specify the specific sequence names on their data. For every subject, only the files with ${nm_seq_type} names specified in the array will be processed. If a subject does not have data for any of the specified sequences, the pipeline will safely ignore it and proceed with the next sequence type.

Script usage

To run the pipeline, execute the run_pipeline.sh script. It will proceed with all subjects in the ${GITHUB_ROOT}/Original folder and create a ${subject_id}-${timepoint}.processed file for each of them upon completion. If a subject has already an associated .processed file, the pipeline will skip this subject and proceed with the next one.

Resulting data

The pipeline will store the resulting data using the following folder structure (which gets automatically created if it does not exist):

${GITHUB_ROOT}
   |
   ---- Registered
           |
           ---- dofs
           ---- MNI_space
           ---- MPRAGE_space
  • dofs contains all the intermediate MIRTK transformations files.
  • MPRAGE_space contains all the intermediate data in T1w structural space.
  • MNI_space contains all the processed data in MNI152 space. This is the data that should be used for further analysis.