Step T1: Generate SRC Files

DSI Studio converts diffusion MRI source data into an SRC file. Current SRC files use the .sz extension; legacy .src.gz files remain supported.

An SRC file stores the diffusion-weighted image volumes together with the b-table and other information needed for reconstruction.

DICOM to SRC

For a single diffusion scan, use Step T1: Open Source Images and select the DICOM folder or files. DSI Studio reads the diffusion information and creates a .sz file.

For larger studies, the Batch Processing functions can organize DICOM files and create SRC files:

• Step B1a: Rename DICOM files — organize selected DICOM files.
• Step B1b: Rename DICOM in Subfolders — organize DICOM studies below a root directory.
• Step B2c: DICOM to SRC/NIFTI — batch-create SRC or NIFTI files.

The DICOM rename functions move/rename files, so keep a backup and test them on a small subset first. See GUI Batch Processing and Rename DICOM CLI.

NIFTI to SRC

A diffusion-weighted NIFTI image needs its diffusion gradient information. DSI Studio commonly reads this from FSL/BIDS bval and bvec sidecars.

For one scan:

1. Click Step T1: Open Source Images and select the 4D diffusion NIFTI file.
2. DSI Studio looks for matching bval and bvec files in the same directory.
3. If they are not found automatically, load them from [Files][Open bval] and [Files][Open bvec].
4. Create the .sz file and inspect the loaded b-table before continuing.

For batch conversion:

• Step B2a: NIFTI to SRC (BIDS) — process a BIDS dataset.
• Step B2b: NIFTI to SRC (Single Folder) — process NIFTI files organized outside BIDS.

For command-line workflows, see SRC Creation CLI.

DSI Studio b-table format

DSI Studio can also read a four-column text b-table:

b-value  bvec-x  bvec-y  bvec-z

Example:

3000 -0.994200 -0.000000 -0.107600
3000 -0.985100 -0.130800  0.111300
3000 -0.985100  0.130800  0.111300

Load it using [Files][Open b-table].

When present in the NIFTI directory, DSI Studio can also use grad_dev.nii.gz for gradient-nonlinearity information and nodif_brain_mask.nii.gz as a brain mask.

Other supported source formats

Bruker 2dseq

Select the 2dseq file in Step T1: Open Source Images. Keep its associated Bruker files in their expected relative directories so DSI Studio can read spatial parameters and the diffusion table.

After loading, verify the image and b-table orientation before reconstruction.

Varian / Agilent FDF

Select the FDF files from the scan directory. DSI Studio reads the image and diffusion-gradient information and creates an SRC file.

Step T1a: Quality Control

Run Diffusion MRI Analysis → Step T1a: Quality Control on the study’s SRC files before reconstruction or population analysis.

The QC report is designed to identify subjects that differ substantially from the rest of the study. Review at least:

• image dimensions and voxel size;
• number of diffusion volumes and shells;
• b-table consistency;
• Neighboring DWI Correlation, which is sensitive to motion, eddy-current artifacts, signal dropout, and other acquisition problems;
• Diffusion Contrast, which summarizes diffusion-weighted signal contrast relevant to resolving fiber orientations;
• any low-quality outlier warning.

A flagged subject should be inspected directly rather than excluded automatically. Determine whether the cause is correctable (for example, an orientation or b-table problem) or reflects acquisition failure that requires exclusion.

The neighboring-DWI-correlation QC method is described in:

Yeh FC, et al. Differential tractography as a track-based biomarker for neuronal injury. NeuroImage 202 (2019): 116131.

See the citation page for the full reference.

B-table orientation

Incorrect b-table orientation produces incorrect fiber orientations. B-table flip/swap operations are available during source creation/reconstruction, but they should be applied only when QC and anatomical inspection indicate a problem.

For batch b-table checking and command-line correction, see Reconstruction CLI.

Isotropic resampling

If isotropic resampling is needed, open the SRC file in Step T2: Reconstruction and use the reconstruction image-editing/resampling tools. Resampling does not add anatomical information and should be used for a specific processing requirement rather than routinely.

See Step T2: Reconstruction.

Combining multiple scans

When multiple diffusion acquisitions were collected in the same image space and should be combined into one SRC file, the command line supports --other_source:

dsi_studio --action=src \
  --source=scan1.nii.gz \
  --other_source=scan2.nii.gz,scan3.nii.gz \
  --output=combined.sz

Do not combine acquisitions that require inter-scan spatial realignment as if they were already in the same image space. Process alignment/motion appropriately for the study design first.