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 other analysis, click [Batch Processing][Step B3: Create SRC files

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

The corresponding command line is the follow:

This command reconstructs an SRC file into the FIB file
dsi_studio --action=rec --source=subject.src.gz --method=4 --param0=1.25 --cmd="[Step T2][Edit][Rotate to MNI2]"

This command tracks a target pathway specified by --track_id 
dsi_studio --action=trk --source=subject.fib.gz --fa_threshold=0 --turning_angle=0 --check_ending=1 --tip_iteration=20 --seed_count=5000000 --tract_count=5000 --track_id=26 --delete_repeat=1 --output=$sujbect.FAT_L.trk.gz --export=stat

The value name list for track_id can be found in /atlas/HCP842_tractography.txt

Comments