5. Retinotopy - Stereo-Boy/Pipeline_AS GitHub Wiki

mrVista basics

How to import a mrVista session from a different computer

Copy the mrVista session folder and start mrVista. Depending on the windows you use, it will ask you: -to localize the inplane nifti to open - this is the functional anatomical (gems) in the nifti folder -to localize the vAnatomy - this is the nu t1 file in the nifti folder -to localize the class file - same folder -to recalculate the gray coords - do it

Navigating mrVista flat patch window

  • ROI(bottom right of window) -> use to see the list of ROIs for this patch. The ROI name that is showing is the one that is currently selected.

  • Use ‘cothresh’ sliding bar on right side to change map threshold

  • Zoom/Reset Zoom buttons are on the bottom left of the window.

  • Left/Right bubble selection on bottom left of window is used to toggle between the left and right hemisphere.

From the toolbar:

File

 -> ROI -> Load ROI (local): opens list of ROI currently saved for this patch, you can select which ones you want to load. Shift+click to select multiple.
 -> Save ROI (local): saves currently selected ROI to ROI folder for this flat patch.
 -> Save All ROIs (local): saves all the ROIs currently loaded to folder.

View

 -> Anatomy and ROIs (no overlay): for anatomical view of flat patch
 -> Parameter Map: for eccentricity map
 -> Phase Map: for phase map

ROI

-> Create -> Create Polygon ROI: to draw and ROI, double click on the original starting point to close the ROI.
-> Delete -> ...: Any ROIs deleted here will still be present in the file folder, so make sure you delete them manually too
-> Add -> …: Add area to ROI that is currently selected in the ROI dropdown menu
-> Remove/Clear -> Remove Polygon: Remove area from currently selected ROI
-> Select/Edit/Combine -> Edit ROI Name/Color: opens a menu that allows you to change the name, color, comments on the ROI. Make sure to check the ‘Save this ROI when done’ box to save your ROI in the file folder. If you change the color of an ROI, you need to go to the other hemisphere and back, or Zoom and Reset Zoom before the color change will appear.
-> Hide/Show ROIs -> Set ROI Options -> set 'ROI Rendering Method' to Filled Perimeter to make patches easier to see
	          -> Hide ROIs: Hides all ROIs on the patch
	          -> Show Which ROIs -> Select display ROIs: allows you to pick from a menu which ROIs you want to see
			         -> Show Selected ROIs: shows only the ROI currently selected
			         -> Show All ROIs: shows all the ROIs on the patch

Color Map (while viewing Phase Map)

-> Rotate/Flip -> Rotate/Flip Using GUI -> change Amount of Rotation on sliding bar and click Accept

Localizing visual retinotopic areas

Localize and orient the calcarine sulcus on the flat patch.

Do this by opening the inflated mesh for the hemisphere and drawing an ROI on the calcarine sulcus. Import it into the gray window, and then into the flat window. For the right hemisphere, orient the flat patch so that the calcarine sulcus is on the left, the superior side of the brain is on top, and the superior side of the brain. For the left hemisphere, the calcarine should be on the right. Use the ImageRotate slider on the bottom of the window to rotate, and View>Flip Flat Patch L/R to flip the flat patch(and its ROIs).

Identifying Retinotopic Areas

The instructions will be for the left hemisphere. To use for the right hemisphere, just replace all mentions of the right horizontal meridian(RHM) with left horizontal meridian(LHM) because each hemisphere will map the contralateral hemifield.

Identifying the saddle

The flat patch should be centered around the occipital pole, which is the center of the parieto-occipital, calcarine, lateral occipital, and intraparietal sulcus(IPS). The saddle is (likely) situated below the occipital pole, and will have erratic patterns in the phase map, and will be foveal in the parameter(eccentricity) map. Most of the other visual areas will branch off of the saddle.

Identifying V1

  • Look at where the calcarine ends near the occipital pole on the anatomical view.
  • Go to the eccentricity map and identify where the more foveal areas are(lower values).
  • Increase the cothresh to >0.1 and remember the areas with the strongest signal. Lower it back down to 0.0001 to get a more comprehensive view of the flat patch.
  • The intersection of these three areas is likely the general vicinity where V1 will be located.
  • Now go to the phase map and near that intersecting area look for a reversal in phases that spans around π radians (around 3). This will be the V1 patch. The phase number at the superior side of the patch will be the value for the lower vertical meridian(LVM) and the phase number at the inferior side of the patch will be the value for the upper vertical meridian(UVM). The phase about halfway between the LVM and the UVM will be the right horizontal meridian(RHM). The ventral and dorsal boundaries of V1 should both be the most extreme values of their respective reversals, with the phase returning to the RHM beyond the boundaries of V1.

Identifying non-IPS areas:

  • The overall pattern of the ROIs(non IPS areas) should follow a horseshoe shape around the saddle.
  • Follow the retinotopic map as shown in the image attached, taken from Larsson and Heeger, 2006. Look for areas in the phase map that have values that smoothly increase, decrease, then increase(or the reverse), also known as reversals. The boundaries of the ROIs should all be located at the peak(lowest or highest) values of these reversals.
  • Use V1 as and anchor and try to draw them so that they have expanding eccentricity values that run perpendicular to their phase changes. Try to draw them in areas of high threshold when possible as these signals will be more reliable.
  • hV4 should be the opposite phase value and progression as V1
  • VO1 and VO2 will likely be in areas of more foveal eccentricity.

Identifying IPS areas:

  • IPS0/V7 should look very similar in phase to LO1. The difference is it extends more upward towards the IPS whereas LO1 extends toward the LO sulcus.
  • Follow the full reversals up the IPS to identify the rest of the areas. An example of what they should look like is shown in the two images taken from Silver et al., 2005.

Additional tips:

  • Making V1 a different color than the rest of the areas will make your life easier when you revisit the flat patches.
  • The ranges and values for the meridians are not set in stone. What is important when drawing areas is that the phase values are internally consistent within the subject. One subject could have a range of 4 radians in between the LVM and UVM, and another could have a range of 2.5. The RHM does not have to be precisely in between the LVM and UVM either, but try to make sure that it is at least 1 radian apart from each.
  • Since prF models are averages, there will be an overrepresentation of the horizontal meridian in the areas. This means that you cannot expect the phases to always fully reach what you have defined as the LVM and UVM in areas where they should. Again, just make sure the values for the meridians are relatively consistent for the subject.
  • When torn between where to draw a flat patch, go with the area that has a reversal with the highest threshold.
  • Shifting the color map for the phase map can do wonders! Green looks the same across an entire radian, so shifting the color map may expose some hidden reversals.
  • A hand drawn reference of the visual areas is included below to help you get a sense of which meridian is located where.