Reconstruction

Reconstruction processes an SRC file (.sz; legacy .src.gz) and creates an FIB file (.fz) for tractography, diffusion measurements, connectome analysis, and other downstream workflows.

Step T2: Open SRC File(s)

Click [Step T2 Reconstruction] in the main window and select one or more SRC files.

Multiple SRC files can be reconstructed as a batch. Processing steps configured on the first file can be applied to the remaining selected files.

Visual quality inspection

Before reconstruction, inspect the raw DWI/source-image view and b-table for obvious problems.

Motion and distortion

Use the b-table/image list to move through the diffusion volumes and look for motion, distortion, signal dropout, or inconsistent slices.

Bad slices

Use Show bad slice to highlight detected problematic slices. Sagittal and coronal views can make slice artifacts easier to identify.

For additional examples, see the quality-control video.

Step T2a: Specify a mask

The reconstruction mask limits processing to the tissue of interest. The mask editor provides thresholding and common morphological operations including smoothing, expansion, erosion, and defragmentation.

A typical starting sequence is Threshold → Smoothing → Defragment, followed by visual inspection and manual correction if needed.

Masks can be saved or loaded as text/NIfTI files.

Corrections and preprocessing

Only apply corrections that are appropriate for the acquisition and study design. Keep the processing consistent across subjects in a group analysis.

TOPUP/EDDY and motion correction

For reverse-phase-encoding acquisitions, use [Corrections][TOPUP/EDDY]. DSI Studio first looks for the matching .rz companion file. If one is not found, it can accept another reverse-phase-encoding .sz, .rz, legacy .src.gz, or NIfTI file.

For acquisitions without a reverse-phase pair, use the applicable EDDY/motion-correction workflow.

These corrections may take substantial processing time. Save the corrected source data as a new .sz file if you want to preserve the corrected dataset for later reconstruction.

Volume orientation correction for animal scans

Animal datasets may need orientation adjustment before template-based analysis. Use Corrections → Volume Orientation Correction to align the volume orientation with the selected template.

When the slice-position slider moves toward the superior end of the volume, the displayed anatomy should follow the orientation expected by the selected template. Use image flip/swap operations only when necessary, and verify the result visually after each change.

Remove background or crop the image volume

Use the image-editing tools to remove irrelevant background signal or crop excessive empty space when appropriate.

Check b-table orientation

An incorrect b-table produces incorrect fiber orientations. Use [B-table][Check b-table] and inspect the result anatomically. Low-SNR or unusual animal acquisitions may require manual verification.

Make isotropic

If needed, resample the source volume to isotropic resolution before reconstruction. Resampling does not add anatomical information, so use it for a specific processing or tracking requirement rather than routinely.

Step T2b: Specify a reconstruction method

Diffusion Tensor Imaging (DTI)

DTI estimates a diffusion tensor and tensor-derived measures such as FA, MD, AD, and RD. It provides one principal tensor direction per voxel and is appropriate when tensor measurements are the intended analysis.

Generalized Q-Sampling Imaging (GQI)

GQI is the standard DSI Studio reconstruction for resolving one or more fiber orientations and is commonly used for native-space tractography.

The diffusion sampling length ratio controls GQI sampling. The appropriate value depends on acquisition and tissue properties. When changing it, verify the resulting fiber orientations and whole-brain tractography rather than selecting a value from the appearance of a single pathway.

Q-Space Diffeomorphic Reconstruction (QSDR)

QSDR reconstructs diffusion information in a selected template space and is commonly used for population, atlas, and connectometry analyses.

Select the template appropriate for the species and study. Inspect registration quality before including a subject in population analysis.

Additional images can be attached when they are needed by the reconstruction/template workflow.

Step T2c: Specify outputs

Select only the additional diffusion measurements needed for the analysis. Available outputs depend on the reconstruction method and DSI Studio version and can include tensor measures, GQI-derived measures, restricted-diffusion measures, and ODF-related outputs.

Saving unnecessary outputs increases .fz file size and processing time.

DTI high-b option

Ignore High b for DTI restricts tensor estimation to lower b-values when appropriate for the acquisition. Use the same rule across subjects in a group study.

Reconstruct

After checking the mask, corrections, reconstruction method, template settings, and requested outputs, start reconstruction. The resulting .fz file can be opened in Step T3: Fiber Tracking or used by the corresponding command-line and population-analysis workflows.

For command-line reconstruction, see Reconstruction CLI.