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fMRI Data Analysis in Slicer (Long version – Use on Workstation with 2G RAM)

This detailed guide walks users through the process of fMRI data analysis using Slicer on workstations with only 2GB of RAM. It covers the essential steps for loading fMRI image sequences, adjusting display settings, setting up paradigms, and modeling signals. By following this step-by-step approach, users can efficiently analyze brain imaging data and prepare results for inspection and interpretation, despite hardware limitations. Perfect for researchers and professionals in neuroimaging, this resource ensures effective analysis without the need for high-end computing.

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fMRI Data Analysis in Slicer (Long version – Use on Workstation with 2G RAM)

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Presentation Transcript

  1. fMRI Data Analysis in Slicer(Long version – Use on Workstation with 2G RAM) Steve Pieper Hiaying Liu Wendy Plesniak Sandy Wells

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

  3. Set Image Display 9: Click Volumes 10: Adjust Win and Lev to Get Best View for the Image 12: First Image in the Sequence 11: Adjust Lo to Mask Out Brain

  4. Select Image Sequence 13: Pick Select Tab 14: Click OK 15: Click Set Window/Level/Thresholds

  5. Design Paradigm 16: Pick Set Up Tab 17: Choose Paradigm Design 18: Click All Runs Are Identical } 21: Input All Values { 22: Click OK } 23: Input All Values 20: Click OK 24: Click OK 19: Input All Values

  6. Model Signal 25: Choose Signal Modeling 26: Choose Box Car 27: Choose HRF 28: Do Not Click Add Temporal Derivative 29: Click Apply to All Conditions 31: Click Fit Model 30: Click OK

  7. View Model 32: Click Vew Model 33: The Model Appears in a Separate Window

  8. Specify Contrasts/Compute 37: Input All Values } 38: Click OK } 34: Choose Contrasts 35: Input All Values 39: Pick Compute Tab 36: Click OK 40: Select Contrasts 41: Click Compute

  9. Inspect 42: Pick Inspect Tab 43: Pick a Volume 44: Click Select 45: Slide the Scale 46: The Activation Overlay

  10. Inspect (cont) 48: Pick a Condition 49: Click a Voxel 47: Click Timecourse 50: The Timecourse for the Condition at the Voxel

  11. Inspect (cont) 51: Click Peristimulus Histogram 52: Click a Voxel (as before) 53: The Peristimulus Histogram 54: Click Any Curve 55: Navigate Intensities for Evs

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