This is automatic pipline that allows to perform Correlation Tractography using DSI Studio from raw ParaVision360 raw data to statistical analysis.
The pipeline is divided into two main components: Preprocessing and Statistical Analysis. Below is an overview of each component and the key scripts involved.
preprocessing.py
This is the main script to execute the preprocessing workflow. During its execution, the script performs several steps to process DTI (Diffusion Tensor Imaging) data obtained from ParaVision360. The script's functionality includes finding and converting Bruker 2dseq files into .src files, reconstructing the data, and creating a DSI Studio database for further statistical analysis.
graph TD;
A[preprocessing.py] --> B[extract_raw_data_bruker.py]
A --> C[reconstruction.py]
A --> D[data_base_creation.py]
B --> B1[STEP T1:
Finds and convert Bruker 2dseq files
to SRC Files and creates directory
based on subject name]
C --> C1[STEP T2:
- Remove background signals or crop image volume;
- Check b-table;
- Motion correction, TOPUP/EDDY;
- Correct image orientation]
C1 --> C2[STEP T3:
- Fiber tracking file FIB creation]
D --> D1[STEP C1:
Aggregates multiple FIB files into a
common template space that
allows group-level analysis]
statistical_analysis.py
This script perform the statistical analysis. It checks for the presence of required directories and files, processes the selected project, and organizes the data for statistical analysis based on demographic information.
graph TD;
A[statistical_analysis.py] --> B[statistical_analysis_pipline.py]
B --> B1[create_statistical_analysis_structure]
B1 --> B1_info[Creates the directory
structure for the statistical analysis
based on the given comparisons.]
B --> B2[parse_demographics]
B2 --> B2_info[Parses the demographics.csv
file to generate comparison pairs
based on unique conditions.]
B --> B3[copy_files_and_update_demographics]
B3 --> B3_info[Copies the source files into
the appropriate directories,
updates demographics information,
runs analysis, and updates the report.]
Follow the installation instructions provided for your operating system. Ensure your environment is set up correctly by following the respective setup guide:
Before running analysis ensure that you have defined a project name and agragated ParaVision360 raw data under the input directory. The preprocessing step involves converting raw DTI data, reconstructing it, and creating a database for further analysis.
Run the Preprocessing Script:
python preprocessing.py
After the preprocessing step and database creation, it's essential to manually verify the quality and accuracy of the generated data. This includes checking for any misregistration or other issues that might have occurred during preprocessing.
- Open DSI Studio and navigate to the STEP C2: View/Edit Connectometry Database.
- Perform visual inspection of all images that were registered
- If misregistration detected please removed it and save Database again inside the same directory
data_base.
The statistical analysis step processes the selected project, organizes data, and performs analysis based on demographic information. Demographic is a file (please use this template) used to run statistical analysis based on condition. Please note that it is inportant to ensure that subject name inside the demographic file matches with names in the same order inside the Database file. If during the Step 3: Manual Check of Database you have detected any issues with registration and removed the subject you need to remove it from Demographic file.
Run the Statistical Analysis Script:
python statistical_analysis.py