Generating SRC files

use –action=src to generate SRC file from NIFTI or DICOM files

Examples

Convert one 4d NIFTI file and generate an SRC file subject001.nii.gz.src.gz

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

Convert one 4d NIFTI file and specify the location of bval and bvec (only needed when DSI Studio cannot find them)

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

*Convert DWI NIFTI files in a BIDS folder and output all SRC files to a folder

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

*Convert DWI NIFTI files in a BIDS session folder and output one SRC file or its reverse phase encoding RSRC file

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

Combine two 4d NIFTI files and generate 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

Search all DICOM files under the assigned directory and output SRC file

dsi_studio --action=src --source=C:\20081006_11_00814348_DWI_WIP_DSI_203 --output=c:\20081006_11_00814348_DWI_WIP_DSI_203.src.gz

Find all *98_AP.nii.gz file and combine its corresponding 99_AP.nii.gz file to generate one combined SRC file

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

Parse all 4d NIFTI files in a folder (each of them has a bval and bvec file that shares a similar file name) and generate corresponding SRC files to a new folder

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

Windows batch file for creating src files from HCP datasets

path=C:\dsi_studio_64
cd F:\HCP\
dir ?????? /b > file_list.txt
for /f "delims=" %%x in (file_list.txt) do (
call dsi_studio.exe --action=src --source=F:\HCP\%%x\T1w\Diffusion\data.nii.gz --output=F:\%%x.src.gz > F:\%%x.txt
)

Windows batch script for creating src from NIFTI data

path=C:\dsi_studio_64
dir ????? /b > file_list.txt
for /f "delims=" %%x in (file_list.txt) do (
call dsi_studio.exe --action=src --source=%%x\%%x_dwi_QCed.nii --bval=%%x\%%x_QC.bval --bvec=%%x\%%x_QC.bvec --output=%%x.src.gz
)

Core Functions

Parameters	Description
source	Specify a directory storing DICOM/NIFTI files or the filename of a 4D NIFTI file

Optional Functions

Parameters	Description
other_source	Specify other files to be included in the SRC file. Multiple files can be assigned using comma separator, (e.g. –other_source=1.nii.gz,2.nii.gz)
output	Assign the output src file name (.src.gz) or the output folder
b_table	Assign the text file to replace b-table
bval	Specify the location of the FSL bval file^a
bvec	Specify the location of the FSL bvec file^a

^afor most cases, DSI Studio can automatically associate bval and bvec with NIFTI automatically.

Accessory Functions

Parameters	Default	Description
recursive	`0`	Search all NIFTI or DICOM files under the directory specified in –source
bids	`0` not bids	Specify whether to use BIDS standard to parse a folder specified by –source
overwrite	`0` no overwrite	Specify whether to overwrite existing files

SRC files Quality Control

use –action=qc to run quality control on SRC files

Examples

Specify a folder storing *.src.gz or *.sz files

dsi_studio --action=qc --source=/folder_storing_src_siles