Generating SRC Files

Use --action=src to generate SRC files from NIFTI or DICOM files.

The src action converts NIFTI or DICOM diffusion data into the current .sz SRC format. Legacy .src.gz files remain supported for compatibility.

Examples

1. Convert a single 4D NIFTI file to an SRC file:

dsi_studio --action=src --source=c:\subject001.nii.gz

2. Specify the location of bval and bvec files for a 4D NIFTI file (when DSI Studio cannot find them automatically):

dsi_studio --action=src --source=c:\subject001.nii.gz --bval=bval --bvec=bvec

3. Convert DWI NIFTI files in a BIDS folder and output all SRC files to a specified folder:

dsi_studio --action=src --source=./bids_root_folder --output=/src_files

4. Parse a BIDS session folder and generate an .sz file, with an .rz companion when reverse-phase data are present:

dsi_studio --action=src --source=./sub-01/ses-01/dwi --bids=1

5. Combine two 4D NIFTI files into one SRC file:

dsi_studio --action=src --source=HCA9992517_V1_MR_dMRI_dir98_AP.nii.gz --other_source=HCA9992517_V1_MR_dMRI_dir99_AP.nii.gz

6. Search a DICOM directory and convert the detected DICOM studies:

dsi_studio --action=src --source=C:\DICOM_folder

For a directory containing no usable NIFTI diffusion data, DSI Studio falls back to its DICOM-directory conversion workflow. That route organizes/converts the detected studies and does not use --output as a single .sz filename.

7. Find and combine specific files based on a pattern to create a combined SRC file:

dsi_studio --action=src --source=*98_AP.nii.gz --other_source=*99_AP.nii.gz

8. Parse 4D NIFTI files from a folder, each with associated bval and bvec files, and generate SRC files in a new folder:

dsi_studio --action=src --source=*.nii.gz --output=/src_folder

9. Batch process using a loop to create SRC files from zip archives and associated files:

dsi_studio --action=src --loop=MGH_*_all.zip --source=mgh_*/diff/preproc/mri/diff_preproc.nii.gz --bval=mgh_*/diff/preproc/bvals.txt --bvec=mgh_*/diff/preproc/bvecs_fsl_moco_norm.txt --output=sub-*_dwi.sz

Core Functions

Parameter Description
source Specify the directory containing DICOM/NIFTI files or the filename of a 4D NIFTI file.

Optional Functions

Parameter Description
other_source Specify additional files to be included in the SRC file. Multiple files can be assigned using a comma-separated list (e.g., --other_source=1.nii.gz,2.nii.gz).
output For single-file or NIFTI/BIDS conversion, assign the output .sz filename or output folder. If not specified, output is written next to the input. The DICOM-directory fallback manages its own output organization rather than treating --output as one .sz filename. Legacy .src.gz remains readable.
b_table Assign a text file to replace the b-table. The file must match the loaded images in size.
bval Specify the location of the FSL bval file. (DSI Studio usually detects this automatically.)
bvec Specify the location of the FSL bvec file. (DSI Studio usually detects this automatically.)
intro Specify a README file to include as an introduction for the SRC file.

Accessory Functions

Parameter Default Description
bids Auto BIDS parsing is selected automatically when a BIDS structure is detected. Use --bids=1 to request BIDS handling explicitly.
overwrite 0 Overwrite existing output files when set to 1.
topup_eddy 0 Run TOPUP and EDDY during directory/BIDS conversion when reverse-phase data are available.
sort_b_table 0 Sort the b-table when creating an SRC file from explicitly supplied images.

Directory behavior

  1. BIDS/NIFTI detection:
    • For a directory source, DSI Studio first looks for BIDS DWI data, then other NIFTI DWI files.
    • --bids=1 can be used to request BIDS handling explicitly.
  2. NIFTI output directory:
    • For directory-based NIFTI/BIDS conversion, --output is an output directory. If omitted, SRC files are written next to the NIFTI inputs.
  3. Reverse phase encoding:
    • Reverse-phase data detected during directory/BIDS conversion are saved as an .rz companion when TOPUP/EDDY is not run during SRC generation.
  4. DICOM fallback:
    • If no NIFTI diffusion data are found under the directory, DSI Studio attempts DICOM conversion using the directory-based DICOM workflow.