Generating SRC Files

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

The src action supports converting NIFTI or DICOM files into SRC format, with optional configurations for b-values, b-vectors, additional sources, and output specifications.

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 one SRC file or its reverse phase encoding RSRC file:

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 all DICOM files under a directory and output an SRC file:

dsi_studio --action=src --source=C:\DICOM_folder --output=C:\output.src.gz

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 Assign the output SRC file name (.src.gz) or the output folder. If not specified, the SRC file will be written to the same directory as the input files.
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
recursive 0 Search for all NIFTI or DICOM files in subdirectories within the specified --source.
bids 0 (not BIDS) Specify whether to use the BIDS standard to parse the folder specified by --source.
overwrite 0 (no overwrite) Specify whether to overwrite existing files.
topup_eddy 0 Specify whether to run topup and eddy correction during SRC generation.
sort_b_table 0 Specify whether to sort the b-table (useful for certain datasets).

Notes from the Source Code

  1. File Search and BIDS Support:
    • The tool can automatically search for NIFTI and DICOM files in the specified --source directory.
    • When --bids=1 is specified, the tool follows the BIDS (Brain Imaging Data Structure) convention for organizing files.
  2. Output Directory:
    • If the --output parameter is not provided, the resulting SRC files are saved in the same directory as the input files.
  3. Reverse Phase Encoding:
    • Reverse phase encoding files can be detected and included automatically in the SRC file generation process.
  4. Error Handling:
    • The tool performs various checks for mismatched b-values, b-vectors, and file compatibility, displaying error messages when issues are encountered.
  5. Default Behavior:
    • If no file is found under the --source, the tool attempts to convert DICOM files to SRC and NIFTI formats.