Wednesday, May 21, 2014

Creating Beta Series Correlation Maps

The last few steps for creating beta series correlation maps is practically identical to what we did before with other functional connectivity maps:

1. Load your beta series map into the AFNI interface and set it as the underlay;
2. Click on "Graph" to scroll around to different voxels and examine different timeseries;
3. Once you find a voxel in a region that you are interested in, write out the timeseries by clicking FIM -> Edit Ideal -> Set Ideal as Center; and then FIM -> Edit Ideal -> Write Ideal to 1D File. (In this case, I am doing it for the right motor cortex, and labeling it RightM1.1D.)
4. Note that you can also average the timeseries within a mask defined either anatomically (e.g., from an atlas), or functionally (e.g., from a contrast). Again, the idea is the same as what we did with previous functional connectivity analyses.
5. Use 3drefit to trick AFNI into thinking that your beta series map is a 3d+time dataset (which by default is not what is output by 3dbucket):

3drefit -TR 2 Left_Betas+tlrc

6. Use 3dfim+ to create your beta series correlation map:

3dfim+ -input Left_Betas+tlrc -polort 1 -ideal_file RightM1.1D -out Correlation -bucket RightM1_BetaSeries

7. Convert this to a z-score map using Fisher's r-to-z transformation:

3dcalc -a Corr_subj01+tlrc -expr 'log((1+a)/(1-a))/2' -prefix Corr_subj01_Z+tlrc

8. Do this for all subjects, and use the results with a second-level tool such as 3dttest++.

9. Check the freezer for HotPockets.

That's it; you're done!

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