Hi Peter,
Thank you for your reply.
I am not sure about CMRR but this data is acquired at MNI Montreal following exactly the same sequence as ADNI3.
Here are my afni_proc command and subsequent commands to generate the connectivity matrix.
afni_proc.py -subj_id $line -dsets /data/data05/Studies/MCSA/RAW/MRI/$line/$RSN -copy_anat /data/data05/Studies/MCSA/RAW/MRI/$line/$T1 -blocks despike align volreg mask regress -tcat_remove_first_trs 10 -volreg_align_e2a -mask_apply epi -mask_segment_anat yes -mask_segment_erode yes -regress_apply_mot_types demean deriv -regress_run_clustsim yes -regress_est_blur_errts
3dresample -master errts.$line.tproject+orig -prefix DKT_resample -input /data/data05/melissa/MCSA_processing/t1_preproc/$line/freesurfer_DKT.nii
@MakeLabelTable -lab_file ../DKT.txt 1 0 -labeltable sub.niml.lt -dset DKT_resample+orig
3dcalc -a DKT_resample+orig -expr 'step(a)' -prefix DKT_mask
3dcalc -a errts.$line.tproject+orig -b DKT_mask+orig -expr 'a*b' -prefix errts_DKT_fs
3dNetCorr -prefix netcorr -mask mask_GM_resam+orig.BRIK -ts_out -fish_z -inset errts_DKT_fs+orig -in_rois DKT_resample+orig -output_mask_nonnull -push_thru_many_zeros -ts_wb_corr -ts_wb_strlabel
fat_mat_sel.py -m netcorr_000.netcc -P "FZ" --A_plotmin=0.27 --B_plotmax=1 --Tight_layout_on --dpi_file=75 -L 2 -d 300 -S 2
