📂 Structural MRI (T1-weighted & T2-weighted)

Preprocessing Steps (summary):

1. Convert to NIfTI – Convert input files to NIfTI format if needed

2. Brain Extraction – Remove non-brain tissue

3. Registration to MNI Space (ANTs: Rigid + Affine) – Align images to the standard MNI template

4. Quality Control (QC) – Automated scoring + visual spot checks

5. Best Scan Selection (SynthSeg) – If multiple scans exist in a session, the highest-quality scan is chosen based on SynthSeg scores

Outputs:

• MNI-aligned images (T1/T2)

• Z-score normalized and cropped versions

• Metadata file with QC scores and best scan flag

📂 Functional MRI (Resting-state fMRI)

Preprocessing Steps (fMRIPrep):

1. BIDS + NIfTI – Organize into BIDS and/or NIfTI format

2. Slice-Timing & Motion Correction – Correct acquisition timing and motion artifacts

3. Normalization to MNI – Spatial normalization to the MNI template

4. Denoising & Smoothing – Apply nuisance regression/filters and smoothing

5. QC & Time-Series Extraction – Generate QC reports and extract ROI-based time series (parcellation)

Outputs:

• MNI-space fMRIPrep derivatives

• ROI time series + connectivity matrices (if enabled)

• QC reports (motion, outliers, quality summaries)

📂 Diffusion Tensor Imaging (DTI)

Preprocessing Steps:

1. DICOM → NIfTI

2. Topup (FSL) – Correct field distortions (if AP/PA available)

3. Eddy (FSL) – Correct motion and eddy currents

4. Brain Extraction (BET) – Remove non-brain tissue

5. Merge Acquisitions – Combine split-session scans if applicable

6. DTI Model Fitting (DTIFIT) – Compute FA, MD, RD, AD maps

7. Registration to MNI (ANTs: Rigid + Affine)

8. QC – Motion metrics, gradient coverage, error maps

Outputs:

• DTI maps (FA/MD/RD/AD) in native and/or MNI space

• Masks, model parameters, and QC reports

Additional Notes

• All intermediate steps are saved for each modality.

• A flowchart is available for all pipelines. For example, DTI:

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