Batch Processing using GUI


Introduction

All processing step in DSI Studio can be applied to a large amount of subject data without using the command line interface. The GUI provides necessary function to batch process subject data using the following steps:

Step B1: Data arrangement


4D NIFTI files


Store the image files (NIFTI or DICOM) by Brain Imaging Data Structure (BIDS, see https://bids.neuroimaging.io/). The image data of each subject should be stored by a folder named by his/her subject ID, and all the folders are placed under a common study folder.



DICOM files


*This function will rename and move files! Please make sure to backup original data before doing this step.*

Use [Batch Processing][Step B1: Rename DICOM files] or [Batch Processing][Step B1: Rename DICOM in Subfoldersto rename and sort DICOM files. DSI Studio should be able to create a folder for each scan and subfolder for each sequence. You can place DICOM files of all subject into one root folder and sort it all at once.

TIP: Try this function with only 2 or 3 subjects and see how the sorting work before applying it to all your data, which can be catastrophic!

Step B2: Create SRC files


Click on [Batch Processing][Step B2: Create SRC files] and select the root study folder that contains all subjects data. DSI Studio will generate an SRC within each subject's folder. I would suggest using searching for all SRC files and placed them together in another folder for further processing.

After DSI Studio processes all data, I highly recommend doing [Diffusion MRI Analysis][QC1: SRC files Quality Control] (see Read DICOM, NIFTI, Bruker 2dseq, or Varian FDF Files) to exclude problematic data.


Step B3: Batch SRC Reconstruction


For the connectometry analysis, please use [Step C1: Reconstruct SRC files for Connecometry] and follow the instructions at Create a connectometry database.

For other analysis, click [Batch Processing][Step B2: Create SRC files


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