Reconstruction

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The reconstruction step processes an SRC file from Step T1 to generate the FIB file, which can be used for advanced analyses like tractography or connectometry.

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Step T2: Open SRC File(s)

Click on the [Step T2 Reconstruction] button in the main project window to select one or multiple SRC files.

DSI Studio will present a reconstruction window as shown below:

Tip: You can batch-reconstruct multiple SRC files. Any preprocessing (e.g., flipping images or aligning to MNI space) applies uniformly to all selected files.

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Visual Quality Inspection (Optional)

Switch to the [Source Images] tab and visually inspect the data for the following issues:

1. Eddy Current Distortion and Motion

• Use the keyboard’s arrow keys to scroll through the b-table list to check for distortions or motion artifacts.

2. Bad Slices

• Click on the [Show bad slices] button to highlight bad slices in red. Use sagittal view for better visibility.

3. Other Problems

• Refer to the video tutorial for detailed guidance.

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Step T2a: Specify a Mask

A mask eliminates background signals, improving reconstruction efficacy. The mask selection window includes tools for:

• Thresholding: Generates an initial selection.
• Smoothing: Smooths the mask contour.
• Expansion: Expands the mask.
• Erosion: Shrinks the mask.
• Defragment: Removes small fragments.

Recommendation: Use thresholding, smoothing, and defragmentation in sequence.

Masks can be saved/loaded as .txt or .nii.gz files.

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Preprocessing Steps

Follow these steps in order to preprocess DWI data effectively:

1. TOPUP/EDDY/Motion Correction

For Reverse-Phase Encoding Acquisition:

1. Click [Corrections][TOPUP/EDDY].
2. Select the reverse-phase encoding file (e.g., *.nii.gz or *.src.gz).
3. DSI Studio will call FSL’s topup and eddy tools for artifact correction.

Without Reverse-Phase Encoding:

1. Click [Corrections][EDDY].
2. FSL’s eddy will correct for eddy current distortions.

Note: This step can take hours. Save a new SRC/SZ file after corrections.

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2. Correct Image Orientations (Animal Scans Only)

Animal scans often require orientation corrections. Use [Corrections][Volume Orientation Correction] to align the volume with the template.

Default template orientations for mice, marmosets, or rhesus are shown below:

If necessary, use [Edit][Image Flip] or [Image Swap] to match the template orientation.

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3. Remove Background Signals or Crop Image Volume (Optional)

Eliminate background noise using [Edit][Erase Background Signals] and crop the volume using [Edit][Crop Background].

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4. Check b-Table Orientation (Animal Scans)

Incorrect b-tables lead to flawed fiber orientations. Use [B-table][Check b-table] to verify b-table orientation. For low SNR datasets, manually test flip/swap configurations.

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5. Make Isotropic (Optional)

Isotropic resolution is crucial for fiber tracking. Use [Edit][Make Isotropic] to interpolate non-isotropic data.

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Step T2b: Specify a Model

Diffusion Tensor Imaging (DTI)

• Generates a single fiber orientation per voxel along with anisotropy and diffusivity measures.
• Use only if GQI fails.

Generalized Q-Sampling Imaging (GQI) (Recommended)

• Model-free method for resolving fiber orientations.
• Optimize the diffusion sampling length ratio (L) using the following steps:
  1. Reconstruct FIB files with different L values (e.g., 0.3, 0.4, …, 2.0).
  2. Inspect crossing and non-crossing regions (e.g., corpus callosum) in [Step T3 Fiber Tracking].

The goal: Select the highest L that minimizes spurious fibers.

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Q-Space Diffeomorphic Reconstruction (QSDR)

• MNI-aligned version of GQI.
• Recommended for analyses in MNI space (e.g., connectometry).
• Ensure your data matches the selected template (e.g., human, monkey, rat).

To transform additional modalities (e.g., T1W) into MNI space, use the [Attach Images…] button.

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Step T2c: Specify Outputs

Specify output metrics (comma-separated) for the FIB file:

• fa: Fractional anisotropy
• rd: Radial diffusivity
• md: Mean diffusivity
• tensor: Tensor matrix (e.g., txx, txy, txz)
• gfa: Generalized fractional anisotropy
• rdi: Restricted diffusion
• odf: Export entire ODF vectors (increases .fib file size).

Advanced Options

• Ignore High b for DTI: Use only b-values <1500 for tensor estimation.

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This documentation captures all key features and workflows for Step T2 Reconstruction in DSI Studio. Let me know if further revisions are needed!