retinotopic mapping workshop
DESCRIPTION
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 - PowerPoint PPT PresentationTRANSCRIPT
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
• 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?
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
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
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.
Help!
http://white.stanford.edu/Wiki.php
http://white.stanford.edu/newlm/index.php/MrVista
Step 1 – The inplane viewAnatomical view
Step 1 – The inplane viewMean fMRI BOLD amplitude map
Step 1 – The inplane viewComputing the correlation analysis
Step 1 – The inplane viewFirst view of phase-encoded data
Step 1 – The inplane viewMultiple slices through the same dataset
Step 1 – The inplane viewDefining an ROI – use CTRL-R or the ‘ROI’ menu
Step 1 – The inplane viewAccessing the plotting tools
Step 1 – The inplane viewA sample fMRI time course
Step 1 – The inplane viewAverage of a single cycle
Step 1 – The inplane viewFFT of a mean time series
Step 1 – The inplane viewFFT of a mean time series after data averaging
Step 1 – The inplane viewPlot single cycle time courses in a set of ROIs down the calcarine sulcus
Step 1 – The inplane viewAveraging time series data across scans
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
Alignmenthttp://white.stanford.edu/newlm/index.php/RxAlign
Alignmenthttp://white.stanford.edu/newlm/index.php/RxAlign
Alignmenthttp://white.stanford.edu/newlm/index.php/RxAlign
Alignmenthttp://white.stanford.edu/newlm/index.php/RxAlign
Alignmenthttp://white.stanford.edu/newlm/index.php/RxAlign
Alignmenthttp://white.stanford.edu/newlm/index.php/RxAlign
Alignmenthttp://white.stanford.edu/newlm/index.php/RxAlign
Alignmenthttp://white.stanford.edu/newlm/index.php/RxAlign
Install segmentation
Install segmentation
Install segmentation
Install segmentation
View data in high-resolution anatomy
Rendering on flat map
Flattening…
Flattening…
Flattening…
Flattening…
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?)
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