Hi, Stef-
The ability to use Alpha+Boxed thresholding with both voxelwise and clusterwise thresholding has now been added to @chauffeur_afni.
If you get the latest version (AFNI_21.2.10 and higher), then you should have this. Here are a couple examples from the help, charmingly both called "E", I now notice... The "trick" with this is that some pieces are specified in specific places---these examples might be the clearest explication of what goes where, but there is also a "Note" in the program's help about it:
[
afni.nimh.nih.gov]
E) Included Clusterizing, with Alpha+Boxed on. Also select the Olay
(idat) and Thr (ithr) volumes descriptively, with subbrick labels.
@chauffeur_afni \
-ulay anat.nii.gz \
-olay stats.nii.gz \
-cbar Reds_and_Blues_Inv \
-clusterize "-NN 1 -clust_nvox 157" \
-func_range 3 \
-set_subbricks -1 "vis#0_Coef" "vis#0_Tstat" \
-thr_olay_p2stat 0.001 \
-thr_olay_pside bisided \
-olay_alpha Yes \
-olay_boxed Yes \
-opacity 7 \
-prefix img_e \
-montx 3 -monty 3 \
-set_xhairs OFF \
-label_mode 1 -label_size 4 \
-no_clean
E) Included Clusterizing, with Alpha+Boxed on, similar to above, but
1sided example.
@chauffeur_afni \
-pbar_posonly \
-ulay anat.nii.gz \
-olay stats.nii.gz \
-cbar "Spectrum:yellow_to_red" \
-clusterize "-NN 1 -clust_nvox 157" \
-func_range 3 \
-set_subbricks -1 1 2 \
-thr_olay 3.314300 \
-thr_olay_pside 1sided \
-olay_alpha Yes \
-olay_boxed Yes \
-opacity 7 \
-prefix img_f \
-montx 3 -monty 3 \
-set_xhairs OFF \
-label_mode 1 -label_size 4 \
-no_clean
Please let me know if anything seems awry.
--pt
