Step T2 Reconstruction
use –action=
recto 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. |
| 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_reso | 2.0 |
specify output resolution for QSDR reconstruction |
| template | 0 |
specify the template for QSDR reconstruction:0:ICBM1521:CIVM_mouse2:Neonate3:INDI_rhesus4:Pitt_Marmoset5:WHS_SD_rat |
Preprocessing Operation
| Parameters | Default | Description |
|---|---|---|
| rev_pe | (empty) | Specify the NIFTI, RSRC, or SRC file of the reversed-phase encoding images for TOPUP/EDDY. specify empty parameter (i.e. ‘–rev_pe’) to automatically search for RSRC or NIFTI files that can be used. |
| volume_correction | 0 (human) 1 (non-human) | Set –volume_correction=1 to apply automatic volume orientation correction by swapping or flipping xyz axis. |
| check_btable | 0 (human) 1 (non-human) | Set –check_btable=1 to test b-table orientation and apply automatic flipping |
| motion_correction | 0 | Set –motion_correction=1 to apply rigid-body transformation to align DWI volumes. The b-table is also rotated accordingly |
| make_isotropic | 2.0 for human scans or slice thickness for nonhuman |
Resample DWI to an isotropic resolution of the specified resolution (i.e. –make_isotropic=2.0) |
| align_acpc | Set –align_acpc=1.5 to rotate image volume to align ap-pc and resample volume to 1.5 mm. |
Additional Operation
| Parameters | Description |
|---|---|
| mask | Specify the mask file (.nii.gz). To use U-Net, specify –mask=unet |
| 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 |
| 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” |
available command list
[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 ACPC]
[Step T2][B-table][flip bx]
[Step T2][B-table][flip by]
[Step T2][B-table][flip bz]
[Step T2][B-table][swap bxby]
[Step T2][B-table][swap bybz]
[Step T2][B-table][swap bxbz]
[Step T2][Edit][Overwrite Voxel Size]=1.0
[Step T2][Edit][Resample]=1.0
[Step T2][Edit][Overwrite Voxel Size]
[Step T2][Corrections][TOPUP EDDY]
[Step T2][Corrections][EDDY]
[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
[Step T2b(2)][Partial FOV]
Accessory Functions
| Parameters | Default | Description |
|---|---|---|
| thread_count | system thread | number of multi-threads 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 |