@ PTaylor - Yes we do have full Fstat, R, T, V, and GLM condition comparison analyses. Not sure which additional output would be of assistance with the FC analysis but please let me know.

For more context: The activation analysis was originally done years and years ago before afni.proc was the primary approach. Specifically we used 3dDeconvolve with DmBlock and AM times (See below). Now we are refining things with a second order analysis.

3dSynthesize is being used here (with the matrix output from that activation 3dDeconvolve) to help isolate specific conditions of interest (by removing the other conditions, motion, and censors) in order to have a cleaner seed signal from which to run an FC correlation analysis with the rest of the brain to investigate the network and connections.

Let me know if this helps clear things up and if any suggestions of how the original deconvolution outputs can be of assistance. Any guidance on correcting for the oddly high correlations very much appreciated as well.

~Dane

------------------------

3dDeconvolve \
-jobs 4 \
-force_TR 2.5 \
-input ${subj}_prepro_all+tlrc \
-mask ${subj}_s4_vr_zp4_cardnudg_e2a_amsk+tlrc \
-censor $censorfile/${subj}_autocensor_AC3VC_pre-moco.1D \
-nfirst 0 \
-polort 16 \
-allzero_OK \
-GOFORIT 3 \
-local_times \
-basis_normall 1 \
-num_stimts 9 \
-num_glt 3 \
-stim_times_AM1 1 $stimdir/${subj}_Strong_stim5c.1D 'dmBLOCK(1)' -stim_label 1 'Strg' \
-stim_times_AM1 2 $stimdir/${subj}_Weak_stim5c.1D 'dmBLOCK(1)' -stim_label 2 'Weak' \
-stim_times_AM1 3 $stimdir/${subj}_Silence_stim5c.1D 'dmBLOCK(1)' -stim_label 3 'Slnc' \
-stim_file 4 $motiondir/${subj}_motion_all.1D'[0]' -stim_label 4 'roll' \
-stim_file 5 $motiondir/${subj}_motion_all.1D'[1]' -stim_label 5 'pitch' \
-stim_file 6 $motiondir/${subj}_motion_all.1D'[2]' -stim_label 6 'yaw' \
-stim_file 7 $motiondir/${subj}_motion_all.1D'[3]' -stim_label 7 'dS' \
-stim_file 8 $motiondir/${subj}_motion_all.1D'[4]' -stim_label 8 'dL' \
-stim_file 9 $motiondir/${subj}_motion_all.1D'[5]' -stim_label 9 'dP' \
-stim_base 4 -stim_base 5 -stim_base 6 -stim_base 7 -stim_base 8 -stim_base 9 \
-gltsym 'SYM: Strg -Weak ' -glt_label 1 Strg_vs_Weak \
-gltsym 'SYM: Strg -Slnc ' -glt_label 2 Strg_vs_Slnc \
-gltsym 'SYM: Weak -Slnc ' -glt_label 3 Weak_vs_Slnc \
-fout -rout -tout -vout -bout -x1D ${subj}_stim5c_dmb.xmat.1D -xjpeg ${subj}_stim5c_dmb.xmat.jpg -full_first -float \
-fitts $subjectsdir/${subj}/${subj}_activationP1_S3_stim5c_dmb_Fitts \
-cbucket $subjectsdir/${subj}/${subj}_activationP1_S3_stim5c_dmb_Cbucket \
-bucket $subjectsdir/${subj}/${subj}_activationP1_S3_stim5c_dmb_Bucket \