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AtlasViewer - Projected Data Onto Cortex - What Am I Looking At?


Jordan Borrell
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Hey Team,

I just have a general question about what data I'm actually seeing projected onto the cortex.  Is it the optical density data?  I'm curious because I've been testing different data analysis methods using Homer3 (v1.26, R2020b) then move over to AtlasViewer (v2.12.4) to project the data onto the cortex, but I'm not seeing much of a difference in the projected data when I change methods of analysis.  If this is the case, then it seems like AtlasViewer will be great to visualize the data before any filters or GLM are conducted on the data.  If someone can verify this or provide the correct interpretation of the process of projecting the data onto the cortex, I'd greatly appreciate it so that I can fully understand this.

Thanks,

Jordan

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Meryem Yücel
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Hi Jordan,

 

I suppose you mean displaying the data on cortex after image reconstruction. Then what you display is either oxy or deoxy Hb changes for the selected condition and HRF time range.

 

Meryem

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Jordan Borrell
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Hey Meryem,

Thank you for the reply!  Yes, I miswrote; it's viewing the Hb changes not concentration data.  After displaying the Hb changes, I wasn't seeing a difference when I changed the analysis process or even parameters in Homer3.  However, I think I figured out the issue.  I deleted all of the files related to AtlasViewer, and I started seeing the differences.  So, I think AtlasViewer was reading the old files.  Do you recommend deleted the old AtlasViewer files (and possibly Homer3 groupResults file) every time I want to change the processing stream or parameters in Homer3, or should the files (groupResults and atlasViewer) files automatically update?

Thanks,

Jordan

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David Boas
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Jordan, I think that you are right that AtlasViewer is not recognizing that Homer has updated the files and thus you are not seeing updated results in AtlasViewer. This has recently been bugging me as well and I want to find a solution as well. I know it is not ideal, but for now you probably need to re-run AtlasViewer to get it to load the new homer results... hopefully we add this capability for AtlasViewer to reload homer results soon.

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