Step T2 Reconstruction

Use --action=rec to perform diffusion reconstruction (e.g., GQI, DTI, QSDR).

This action reconstructs diffusion data (SRC/SZ format) into FIB files, with preprocessing corrections, masking, and registration options.

Examples

1. Reconstruct all SRC files with GQI using a 1.25 sampling length and write .fib files to fib/:

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

2. Reconstruct a single SRC file after EDDY correction:

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

3. Reconstruct after TOPUP+EDDY using a reverse-PE b0 in a NIfTI file:

dsi_studio --action=rec --source=*.sz \
            --rev_pe=*_rev_b0.nii.gz \
            --method=4 --param0=1.25

4. Apply TOPUP+EDDY only (no reconstruction) and save the corrected SRC:

dsi_studio --action=rec --source=raw_dwi.sz \
            --rev_pe=rev_b0.nii.gz \
            --save_src=raw_dwi_proc.sz

5. Perform QSDR reconstruction with a 1.25 sampling ratio, warping both T1w and T2w images:

dsi_studio --action=rec --source=subj1.sz \
            --method=7 \
            --param0=1.25 \
            --other_image=t1w:my_t1w.nii.gz,t2w:my_t2w.nii.gz

6. Bash loop to QSDR-reconstruct every .sz file with ODF output:

#!/bin/bash
exec 1>log_qsdr.out 2>&1
method=7            # 7 = QSDR
param0="1.25"
for sub in *.sz; do
  echo
  dsi_studio --action=rec \
              --source="$sub" \
              --method=$method \
              --param0=$param0 \
              --odf_resolving=1
  echo
done

Core Reconstruction Options

Option Default Description
--source (required) Path to the .sz (or .src.gz) file to reconstruct.
--method 4 Reconstruction algorithm:
1=DTI, 4=GQI, 7=QSDR.
--param0 1.25 (in vivo) / 0.6 (ex vivo) Primary diffusion sampling length (for GQI/QSDR).
--param1 method-specific Second method parameter (e.g., order, regularization).
--param2 method-specific Third method parameter.
--odf_resolving 0 Enable ODF resolving during reconstruction.
--thread_count System thread count Number of threads used for reconstruction.
--template 0 QSDR template index (see printed list at startup—e.g. 0=ICBM152, 1=CIVM_mouse, etc.).
--qsdr_reso 2.0 mm Output resolution for QSDR (overridden if smaller than your voxel size).
--r2_weighted 0 Use R²-weighted SDF estimation for GQI/QSDR.
--other_output fa,rd,rdi Comma-separated list of diffusion metrics to compute. Add odf for ODF data; use all for every possible measure.

Preprocessing Options

Option Default Description
--rev_pe (auto-detect) NIfTI, RSRC, or SRC of the reverse-phase-encoding b0 for TOPUP/EDDY.
--volume_correction 0 Apply automatic volume orientation correction (swap/flip axes).
--check_btable 0 Run b-table QC and auto-flip/swaps to fix gradient directions.
--correct_by_t2 (none) Perform susceptibility distortion correction by nonlinearly warping b0 → T2w.
--motion_correction 0 Rigid-body align DWI volumes (and rotate b-table accordingly).
--make_isotropic (none) Resample DWI to isotropic resolution; defaults to 2.0 mm for human or your native slice thickness for non-human.
--align_acpc (none) Rotate/resample volume to align AC–PC; specify target isotropic resolution (e.g., --align_acpc=1.5).

Masking & Registration Options

Option Description
--mask Path to a brain mask (.nii.gz).
Use --mask=unet to run U-Net segmentation, or --mask=template.
--apply_mask If set, applies the loaded mask during reconstruction (useful after reloading via --save_src or --save_nii).
--rotate_to Rigid-body rotate DWI into the specified T1w/T2w space (no scaling).
--align_to Affine align DWI into the specified T1w/T2w space (includes scaling/shearing).
--other_image Attach native-space images for QSDR to bring to template space. Format: t1w:/path/t1w.nii.gz,t2w:/path/t2w.nii.gz.

I/O & Miscellaneous

Option Description
--output Output folder or filename prefix for reconstructed files.
--save_src Write out the preprocessed SRC (no reconstruction).
--save_nii Write out the preprocessed 4D NIfTI instead of SRC.
--intro Load a text file (.txt/.md) as the “introduction” for embedding in the reconstruction report.
--remove Comma-list or ranges of DWI indices to drop—e.g., --remove=0,5:10,end.
--export_r Write a .rXX file reporting registration R² (e.g., .r85 for 0.85).
--cmd Chain GUI steps for extra edits: e.g., --cmd="[Step T2][Resample]=1.0+[Step T2][File][Save Src File]=out.sz".

Available [Step …] commands in --cmd

The following commands are defined in libs/dsi/image_model.cpp and can be chained using --cmd:

File Operations

Corrections

Editing

B-table Operations

This comprehensive documentation includes all available options and commands for --action=rec. Let me know if further refinements are needed!