Step T2 Reconstruction

use –action=rec to initiate fiber tracking in DSI Studio

Examples

Reconstruct all SRC files with GQI using 1.25 mean diffusion distance and output all FIB files to a folder named fib

dsi_studio --action=rec --source=*.src.gz --method=4 --param0=1.25 --output=/fib/

*Reconstruct all SRC files after EDDY correction

dsi_studio --action=rec --source=subject1.src.gz --cmd="[Step T2][Corrections][EDDY]" --method=4 --param0=1.25

Reconstruct SRC file after TOPUP/EDDY correction using reverse-phase encoding b0 stored in the nifti file.

dsi_studio --action=rec --source=*.src.gz --rev_pe=*.rev_b0.nii.gz --method=4 --param0=1.25

Apply TOPUP/EDDY to the src file using the corresponding reverse PE image and save the preprocessed data to a new SRC file (no reconstruction done).

dsi_studio --action=rec --source=*_s04_dMRI_dir258_1_HDFT.src.gz --rev_pe=*_s09_dMRI_dir258_2_HDFT.nii.gz --save_src=*_proc.src.gz

QSDR reconstruction with 1.25 sampling length ratio. The t1w and t2w were also warped with QSDR

dsi_studio --action=rec --source=20081006_M025Y_1Shell.src.gz --method=7 --other_image=t1w:my_tiw.nii.gz,t2w:my_t2w.nii.gz

A bash script that reconstructs all src.gz files in the directory

#!/bin/bash
# Reconstruct all src.gz file in the directory
# Output logging
exec 1>log_qsdr.out 2>&1

# List all src.gz files
subs=$(ls *.src.gz)

# Reconstruction Parameters
method=7          # 7 for QSDR
param0="1.25"

for sub in $subs
do
    echo
        dsi_studio --action=rec --source=${sub} --method=${method} --param0=${param0} --record_odf=1
    echo
done

Core Functions

Parameters Default Description
source   specify the .src.gz file for reconstruction.
method 4 specify the reconstruction methods.
0:DSI, 1:DTI, 4:GQI 7:QSDR.
param0 1.25 (in-vivo) or 0.6 (ex-vivo) the diffusion sampling length ratio for GQI and QSDR reconstruction.
align_acpc 1 rotate image volume to align ap-pc.
check_btable 1 specify whether the b-table orientation will be checked and automatically flipped
other_output fa,ad,rd,md,nqa,iso,rdi,nrdi specify what diffusion metrics to calculate. use all to get all of possible metrics
record_odf 0 specify whether to output the ODF in the fib file (used in connectometry analysis).
QSDR Parameters Default Description
qsdr_reso dwi resolution specify output resolution for QSDR reconstruction
template 0 specify the template for QSDR reconstruction:
0:ICBM152
1:CIVM_mouse
2:Neonate
3:INDI_rhesus
4:Pitt_Marmoset
5:WHS_SD_rat

Optional Functions

Parameters Description
mask specify the mask file (.nii.gz). To use U-Net, specify –mask=unet
rev_pe specify the NIFTI or SRC file of the reversed-phase encoding images for TOPUP/EDDY
rotate_to specify a T1W or T2W for DSI Studio to rotate DWI to its space. (no scaling or shearing)
align_to specify a T1W or T2W for DSI Studio to use affine transform to its space. (including scaling or shearing)
other_image assign other image volumes (e.g., T1W, T2W image) to be wrapped with QSDR. –other_image=
save_src save preprocessed images to a new SRC file
save_nii save preprocessed images back to 4d NIFTI file
motion_correction apply rigid-body transformation to align DWI volumes. The b-table is also rotated accordingly
cmd specify any of the following commands for preprocessing. Use “+” to combine commands, and use “=” to assign value/parameters (e.g. –cmd=”[Step T2][Corrections][EDDY]+[Step T2][Edit][Overwrite Voxel Size]=1.0” 
 [Step T2][File][Save 4D NIFTI]
 [Step T2][File][Save Src File]
 [Step T2][Edit][Image flip x]
 [Step T2][Edit][Image flip y]
 [Step T2][Edit][Image flip z]
 [Step T2][Edit][Image swap xy]
 [Step T2][Edit][Image swap yz]
 [Step T2][Edit][Image swap xz]
 [Step T2][Edit][Crop Background]
 [Step T2][Edit][Smooth Signals]
 [Step T2][Edit][Align APPC]
 [Step T2][Edit][Change b-table:flip bx]
 [Step T2][Edit][Change b-table:flip by]
 [Step T2][Edit][Change b-table:flip bz]
 [Step T2][Edit][Overwrite Voxel Size]=1.0
 [Step T2][Edit][Resample]=1.0
 [Step T2][Edit][Overwrite Voxel Size]
 [Step T2][B-table][flip bx]
 [Step T2][B-table][flip by
 [Step T2][Corrections][TOPUP EDDY]
 [Step T2][Corrections][EDDY]
 [Step T2][B-table][flip bz]
 [Step T2a][Open]     # specify mask
 [Step T2a][Smoothing]
 [Step T2a][Defragment]
 [Step T2a][Dilation]
 [Step T2a][Erosion]
 [Step T2a][Negate]
 [Step T2a][Remove Background]
 [Step T2a][Threshold]=100

Accessory Functions

Parameters Default Description
thread_count system thread number of multi-thread used to conduct reconstruction
dti_no_high_b 1 for human data, 0 for animal data specify whether the construction of DTI should ignore high b-value (b>1500)
r2_weighted 0 specify whether GQI and QSDR uses r2-weighted to calculate SDF