open-discussion > RE: Improving visualization of clusters in MRIcroGL - Finding corresponding AFNI colormap "Reds_and_blues_Inv" in MRIcroGL?
Jul 10, 2024  04:07 PM | Chris Rorden
RE: Improving visualization of clusters in MRIcroGL - Finding corresponding AFNI colormap "Reds_and_blues_Inv" in MRIcroGL?

I would suggest you look at the documentation


  https://www.nitrc.org/plugins/mwiki/inde...


First of all, it really helps visualization if you load an unthresholded image as an overlay, and subsequently apply a thresholding value (the minmax range). When you threshold an image, you artificially set all non-significant voxels to be zero, and since the data is smooth the surviving clusters are surrounded by neighbors of zeros instead of near-threshold values. This causes artificially dark interpolation.


The other option is to use nearest neighbor interpolation, which will cause jagged images:


gl.overlayloadsmooth(0)


The scripting/templates/jagged menu item illustrates this issue.


 

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TitleAuthorDate
benedetta cecconi Jul 10, 2024
RE: Improving visualization of clusters in MRIcroGL - Finding corresponding AFNI colormap "Reds_and_blues_Inv" in MRIcroGL?
Chris Rorden Jul 10, 2024
benedetta cecconi Jul 11, 2024