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Retinotopic mapping workshop

Retinotopic mapping workshop. COSMO 2012. Starting materials. In the folder ‘COSMO’ you will find raw data and toolboxes – as if you had just finished an fMRI retino mapping scan

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Retinotopic mapping workshop

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  1. Retinotopic mapping workshop COSMO 2012

  2. Starting materials • In the folder ‘COSMO’ you will find raw data and toolboxes – as if you had just finished an fMRI retino mapping scan • Your mission is to process these data to the stage where you can see phase-encoded retinotopy on the cortical surface. • How many visual areas can you delineate?

  3. Stages I • Examine raw (aligned) data • Average time series • Compute coherence / phase maps • Visualize data in the ‘Inplane’ view • Plot (and understand) time series from different parts of the brain

  4. Stages II • Compute alignment between ‘Inplanes’ and a high resolution reference anatomy • Project data into this ‘Gray’ view • Find the calcarine sulcus. Plot times series along this anatomical feature • Render the surface of the brain as a 3D mesh • Project retinotopy data to this surface. • Inflate the surface

  5. Stages III • Create flattened representations of the left and right occipital cortex • Project data to ‘Flat maps’ • Identify the borders of visual areas. • Create and label ROIs around these areas • Project these ROIs back to th Gray view • Render them.

  6. Help! http://white.stanford.edu/Wiki.php http://white.stanford.edu/newlm/index.php/MrVista

  7. Step 1 – The inplane view Anatomical view

  8. Step 1 – The inplane view Mean fMRI BOLD amplitude map

  9. Step 1 – The inplane view Computing the correlation analysis

  10. Step 1 – The inplane view First view of phase-encoded data

  11. Step 1 – The inplane view Multiple slices through the same dataset

  12. Step 1 – The inplane view Defining an ROI – use CTRL-R or the ‘ROI’ menu

  13. Step 1 – The inplane view Accessing the plotting tools

  14. Step 1 – The inplane view A sample fMRI time course

  15. Step 1 – The inplane view Average of a single cycle

  16. Step 1 – The inplane view FFT of a mean time series

  17. Step 1 – The inplane view FFT of a mean time series after data averaging

  18. Step 1 – The inplane view Plot single cycle time courses in a set of ROIs down the calcarine sulcus

  19. Step 1 – The inplane view Averaging time series data across scans

  20. Alignment • Purpose: Compute an affine transformation between the ‘Inplane’ anatomical data and a high-resolution anatomical dataset. • Segmentation, mesh generation has been performed on the highres anatomy already • If all functional datasets are transformed into this space then data from different expt on the same subject can be compared

  21. Alignment http://white.stanford.edu/newlm/index.php/RxAlign

  22. Alignment http://white.stanford.edu/newlm/index.php/RxAlign

  23. Alignment http://white.stanford.edu/newlm/index.php/RxAlign

  24. Alignment http://white.stanford.edu/newlm/index.php/RxAlign

  25. Alignment http://white.stanford.edu/newlm/index.php/RxAlign

  26. Alignment http://white.stanford.edu/newlm/index.php/RxAlign

  27. Alignment http://white.stanford.edu/newlm/index.php/RxAlign

  28. Alignment http://white.stanford.edu/newlm/index.php/RxAlign

  29. Install segmentation

  30. Install segmentation

  31. Install segmentation

  32. Install segmentation

  33. View data in high-resolution anatomy

  34. Rendering on flat map

  35. Flattening…

  36. Flattening…

  37. Flattening…

  38. Flattening…

  39. This is the end… • Or in fact the beginning • How many visual areas can you find? • Define ROIs around some of them (use the polygon ROI tool) • Plot some statistics (co vs phase?)

  40. More • Transform ROIs back into the Gray view. • Build and render a 3D mesh in this view (you will have to find and run mrmMeshSrv.exe first) • Look at data on the inflated mesh • Extract voxel-level data from an ROI

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