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Comprehensive Guide to fMRI Data Analysis in Slicer

This guide provides a detailed walkthrough for conducting fMRI data analysis using Slicer software, covering key steps from loading image sequences to model fitting and inspection. Users will learn how to navigate through the ibrowser, apply filters, reorient images, set up design paradigms, and compute contrasts effectively. Each step is outlined with clear instructions to ensure ease of understanding, making it suitable for both beginners and experienced practitioners in neuroimaging research. Enhance your data processing skills with this comprehensive tutorial.

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Comprehensive Guide to fMRI Data Analysis in Slicer

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  1. fMRI Data Analysis in Slicer Steve Pieper Haiying Liu Wendy Plesniak Sandy Wells

  2. Load Image Sequence 1: Go to Ibrowser Module 2: Pick Load Tab 3: Click File Browse 4: Pick Any File 5: Click Load Multiple Files 6: Input a Filter 7: Input a Sequence Name 8: Click Apply

  3. Reorient Image Sequence 9: Pick Process Tab 10: Click Flip S/I

  4. Set Image Display 11: Click Volumes 12: Adjust Win and Lev to Get Best View for the Image 14: First Image in the Sequence 13: Adjust Lo to Mask Out Brain

  5. Select Image Sequence 16: Pick Select Tab 17: Click OK 15: Go to fMRIEngine Module 18: Click Set Window/Level/Thresholds

  6. Design Paradigm 19: Pick Set Up Tab 20: Choose Paradigm Design } 21: Input All Values 22: Click OK

  7. Model Signal 23: Choose Signal Modeling 24: Choose Box Car 25: Choose HRF 26: Do Not Click Add Temporal Derivative 27: Click Apply to All Conditions 29: Click Fit Model 28: Click OK

  8. View Model 30: Click Vew Model 31: The Model Appears in a Separate Window

  9. Specify Contrasts/Compute 32: Choose Contrasts 33: Input All Values } 34: Click OK 35: Pick Compute Tab 36: Select Contrast 37: Click Compute

  10. Inspect 38: Pick Inspect Tab 39: Pick a Volume 40: Click Select 41: Slide the Scale 42: The Activation Overlay

  11. Inspect (cont) 44: Pick a Condition 45: Click a Voxel 43: Click Timecourse 46: The Timecourse for the Condition at the Voxel

  12. Inspect (cont) 47: Click Peristimulus Histogram 48: Click a Voxel (as before) 49: The Peristimulus Histogram 50: Click Any Curve 51: Navigate Intensities for Evs

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