Retinotopic mapping workshop
description
Transcript of Retinotopic mapping workshop
![Page 1: Retinotopic mapping workshop](https://reader035.fdocuments.in/reader035/viewer/2022081520/56816763550346895ddc3f39/html5/thumbnails/1.jpg)
Retinotopic mapping workshop
COSMO 2012
![Page 2: Retinotopic mapping workshop](https://reader035.fdocuments.in/reader035/viewer/2022081520/56816763550346895ddc3f39/html5/thumbnails/2.jpg)
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?
![Page 3: Retinotopic mapping workshop](https://reader035.fdocuments.in/reader035/viewer/2022081520/56816763550346895ddc3f39/html5/thumbnails/3.jpg)
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
![Page 4: Retinotopic mapping workshop](https://reader035.fdocuments.in/reader035/viewer/2022081520/56816763550346895ddc3f39/html5/thumbnails/4.jpg)
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
![Page 5: Retinotopic mapping workshop](https://reader035.fdocuments.in/reader035/viewer/2022081520/56816763550346895ddc3f39/html5/thumbnails/5.jpg)
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.
![Page 6: Retinotopic mapping workshop](https://reader035.fdocuments.in/reader035/viewer/2022081520/56816763550346895ddc3f39/html5/thumbnails/6.jpg)
Help!
http://white.stanford.edu/Wiki.php
http://white.stanford.edu/newlm/index.php/MrVista
![Page 7: Retinotopic mapping workshop](https://reader035.fdocuments.in/reader035/viewer/2022081520/56816763550346895ddc3f39/html5/thumbnails/7.jpg)
Step 1 – The inplane viewAnatomical view
![Page 8: Retinotopic mapping workshop](https://reader035.fdocuments.in/reader035/viewer/2022081520/56816763550346895ddc3f39/html5/thumbnails/8.jpg)
Step 1 – The inplane viewMean fMRI BOLD amplitude map
![Page 9: Retinotopic mapping workshop](https://reader035.fdocuments.in/reader035/viewer/2022081520/56816763550346895ddc3f39/html5/thumbnails/9.jpg)
Step 1 – The inplane viewComputing the correlation analysis
![Page 10: Retinotopic mapping workshop](https://reader035.fdocuments.in/reader035/viewer/2022081520/56816763550346895ddc3f39/html5/thumbnails/10.jpg)
Step 1 – The inplane viewFirst view of phase-encoded data
![Page 11: Retinotopic mapping workshop](https://reader035.fdocuments.in/reader035/viewer/2022081520/56816763550346895ddc3f39/html5/thumbnails/11.jpg)
Step 1 – The inplane viewMultiple slices through the same dataset
![Page 12: Retinotopic mapping workshop](https://reader035.fdocuments.in/reader035/viewer/2022081520/56816763550346895ddc3f39/html5/thumbnails/12.jpg)
Step 1 – The inplane viewDefining an ROI – use CTRL-R or the ‘ROI’ menu
![Page 13: Retinotopic mapping workshop](https://reader035.fdocuments.in/reader035/viewer/2022081520/56816763550346895ddc3f39/html5/thumbnails/13.jpg)
Step 1 – The inplane viewAccessing the plotting tools
![Page 14: Retinotopic mapping workshop](https://reader035.fdocuments.in/reader035/viewer/2022081520/56816763550346895ddc3f39/html5/thumbnails/14.jpg)
Step 1 – The inplane viewA sample fMRI time course
![Page 15: Retinotopic mapping workshop](https://reader035.fdocuments.in/reader035/viewer/2022081520/56816763550346895ddc3f39/html5/thumbnails/15.jpg)
Step 1 – The inplane viewAverage of a single cycle
![Page 16: Retinotopic mapping workshop](https://reader035.fdocuments.in/reader035/viewer/2022081520/56816763550346895ddc3f39/html5/thumbnails/16.jpg)
Step 1 – The inplane viewFFT of a mean time series
![Page 17: Retinotopic mapping workshop](https://reader035.fdocuments.in/reader035/viewer/2022081520/56816763550346895ddc3f39/html5/thumbnails/17.jpg)
Step 1 – The inplane viewFFT of a mean time series after data averaging
![Page 18: Retinotopic mapping workshop](https://reader035.fdocuments.in/reader035/viewer/2022081520/56816763550346895ddc3f39/html5/thumbnails/18.jpg)
Step 1 – The inplane viewPlot single cycle time courses in a set of ROIs down the calcarine sulcus
![Page 19: Retinotopic mapping workshop](https://reader035.fdocuments.in/reader035/viewer/2022081520/56816763550346895ddc3f39/html5/thumbnails/19.jpg)
Step 1 – The inplane viewAveraging time series data across scans
![Page 20: Retinotopic mapping workshop](https://reader035.fdocuments.in/reader035/viewer/2022081520/56816763550346895ddc3f39/html5/thumbnails/20.jpg)
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
![Page 21: Retinotopic mapping workshop](https://reader035.fdocuments.in/reader035/viewer/2022081520/56816763550346895ddc3f39/html5/thumbnails/21.jpg)
Alignmenthttp://white.stanford.edu/newlm/index.php/RxAlign
![Page 22: Retinotopic mapping workshop](https://reader035.fdocuments.in/reader035/viewer/2022081520/56816763550346895ddc3f39/html5/thumbnails/22.jpg)
Alignmenthttp://white.stanford.edu/newlm/index.php/RxAlign
![Page 23: Retinotopic mapping workshop](https://reader035.fdocuments.in/reader035/viewer/2022081520/56816763550346895ddc3f39/html5/thumbnails/23.jpg)
Alignmenthttp://white.stanford.edu/newlm/index.php/RxAlign
![Page 24: Retinotopic mapping workshop](https://reader035.fdocuments.in/reader035/viewer/2022081520/56816763550346895ddc3f39/html5/thumbnails/24.jpg)
Alignmenthttp://white.stanford.edu/newlm/index.php/RxAlign
![Page 25: Retinotopic mapping workshop](https://reader035.fdocuments.in/reader035/viewer/2022081520/56816763550346895ddc3f39/html5/thumbnails/25.jpg)
Alignmenthttp://white.stanford.edu/newlm/index.php/RxAlign
![Page 26: Retinotopic mapping workshop](https://reader035.fdocuments.in/reader035/viewer/2022081520/56816763550346895ddc3f39/html5/thumbnails/26.jpg)
Alignmenthttp://white.stanford.edu/newlm/index.php/RxAlign
![Page 27: Retinotopic mapping workshop](https://reader035.fdocuments.in/reader035/viewer/2022081520/56816763550346895ddc3f39/html5/thumbnails/27.jpg)
Alignmenthttp://white.stanford.edu/newlm/index.php/RxAlign
![Page 28: Retinotopic mapping workshop](https://reader035.fdocuments.in/reader035/viewer/2022081520/56816763550346895ddc3f39/html5/thumbnails/28.jpg)
Alignmenthttp://white.stanford.edu/newlm/index.php/RxAlign
![Page 29: Retinotopic mapping workshop](https://reader035.fdocuments.in/reader035/viewer/2022081520/56816763550346895ddc3f39/html5/thumbnails/29.jpg)
Install segmentation
![Page 30: Retinotopic mapping workshop](https://reader035.fdocuments.in/reader035/viewer/2022081520/56816763550346895ddc3f39/html5/thumbnails/30.jpg)
Install segmentation
![Page 31: Retinotopic mapping workshop](https://reader035.fdocuments.in/reader035/viewer/2022081520/56816763550346895ddc3f39/html5/thumbnails/31.jpg)
Install segmentation
![Page 32: Retinotopic mapping workshop](https://reader035.fdocuments.in/reader035/viewer/2022081520/56816763550346895ddc3f39/html5/thumbnails/32.jpg)
Install segmentation
![Page 33: Retinotopic mapping workshop](https://reader035.fdocuments.in/reader035/viewer/2022081520/56816763550346895ddc3f39/html5/thumbnails/33.jpg)
View data in high-resolution anatomy
![Page 34: Retinotopic mapping workshop](https://reader035.fdocuments.in/reader035/viewer/2022081520/56816763550346895ddc3f39/html5/thumbnails/34.jpg)
Rendering on flat map
![Page 35: Retinotopic mapping workshop](https://reader035.fdocuments.in/reader035/viewer/2022081520/56816763550346895ddc3f39/html5/thumbnails/35.jpg)
Flattening…
![Page 36: Retinotopic mapping workshop](https://reader035.fdocuments.in/reader035/viewer/2022081520/56816763550346895ddc3f39/html5/thumbnails/36.jpg)
Flattening…
![Page 37: Retinotopic mapping workshop](https://reader035.fdocuments.in/reader035/viewer/2022081520/56816763550346895ddc3f39/html5/thumbnails/37.jpg)
Flattening…
![Page 38: Retinotopic mapping workshop](https://reader035.fdocuments.in/reader035/viewer/2022081520/56816763550346895ddc3f39/html5/thumbnails/38.jpg)
Flattening…
![Page 39: Retinotopic mapping workshop](https://reader035.fdocuments.in/reader035/viewer/2022081520/56816763550346895ddc3f39/html5/thumbnails/39.jpg)
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?)
![Page 40: Retinotopic mapping workshop](https://reader035.fdocuments.in/reader035/viewer/2022081520/56816763550346895ddc3f39/html5/thumbnails/40.jpg)
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