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: Renaming DICOM


Skip this step if you have NIFTI 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 Differential tractography for longitudinal data, you may use [Step T2 Reconstriuction] and select all baseline SRC files. Then at [Step T2B(2)][Advance Options][Compare SRC] select only the SRC file that matches the current loading SRC files (file name shown on the top window). For the rest SRC files, DSI Studio will find the best matching follow-up scans (make sure to put them in the same directory)(Versions after 1/12/2021).

For other analysis, click [Batch Processing][Step B3: SRC to FIB

Step B4: Automatic Fiber Tracking


After the SRC files are created, click on [Batch Processing][Step B4: Create SRC files


Click on the [Open] button and select SRC files. In Step B4(b), select target pathways to run automatic fiber tracking.

GQI length ratio: it is the "diffusion sampling length ratio" used in GQI reconstruction. The value controls the sensitivity to restricted diffusion
Resample DWI: the original DWI will be resampled to either 2 mm or 1mm. Even if the data are acquired at 2mm, it is still recommended to resample DWI.
Tract count: the final track count for each pathway. Higher value takes more times.
Pruning count: pruning removal noisy pathways that are likely to be false connections

Comments