Instructions

01_extract_data.ipynb

• Helper file to extract .zip and .rar files and also instantly change the folder names to the respective pseudonyms (eg. IN01234N13).
• Input:
  • inputDir -> String: Path to folder that contains the zip (and/or rar) files.
  • outputDir -> String: Prefered folder where the DICOM folders are stored.

02_create_nifti.ipynb

• Helper file to convert DICOMs to NIFTIs using dcm2niix
• PLEASE NOTE: THE SCRIPT DELETES ALL FOLDERS EXCEPT RESTING-STATE AND sT1W_3D_TFE_SENSE TO SAVE DISK SPACE !!!!
• Also enables automatic transfer of the T1w Images to the target folder for DPABI: T1Img. Note: This is commented and thus deactivated by default.
• Input:
  • base_path -> String: Path to DICOMS which is the outputDir from 01_extract_data.ipynb.
  • outputPath -> String: Target folder for the converted NIFTIs.

03_conversion.m

• MATLAB script to convert the 3D rs-fMRI files to one 4D image.
• Input:
  • base_path -> String: Path to NIFTIs which is the outputPath from 02_create_nifti.ipynb.
  • outputPath -> String: Target folder for the converted NIFTIs. This should also be the base folder for DPABI Toolbox ending FunImg

Continue in DPABI:

• Make sure the 4D functional images are saved in a folder FunImg and the T1w structural images are saved in T1Img. This is MANDATORY!
• These folders should contain one folder per subject
• See this document on rfmri.org/Course for more information.