AFNI 8 Class Notes: 6/30/2016 [12/15/2025]

After you have Group Analysis Complete you can open the AFNI gui: afni

From here you can:

1. set the Underlay and Overlay.
2. open Define Overlay.
3. select OLay and Thr.
4. set the voxel-based p-value (right click on the T-t text).
5. set the cluster-based (alpha threshold) based on ClustSim determinations.
6. press Rpt to get table.
7. change output file prefix.
8. press SaveTable and SaveMsk.
9. on Axial/Sagittal/Coronal views select Disp select jpg.
10. press Sav1.jpg and enter good naming

To make nice surface rendered images in afni use an approach like: do_suma

To get make tables use an approach like: TableFillerTLRC or TableFillerMNI

To get extractions on the clusters use 3dROIstats examples:

• 3dROIstats -mask {output file prefix}_mask+tlrc ../Subjects/*BRIKS/*{task}+tlrc > output.ROIS.txt
•  awk 'NR>1{print "\x27"$NF"\x27"}' dataTable_CSPvCSM_AcqvRet | xargs -L9999 3dROIstats -mask Clust_task_mask+tlrc. > Clust_task_extract.txt

You can then look at data in R if you wish:  peakingAtData.R