Hi!

Thanks! I just realized that the stats.REML file had all my contrasts! But the standard (3dDeconvolve) stats file does also have my contrasts and it seems like the regression is run there as well. Are you absolutely sure that the regression is also not preformed in the 3dDeconvolve part? The proc script does have the large 3dDeconvolve part with all stimfiles and outputs it to stats.$subj. This would be quite nice since I would have both non-ANATICORED results and ANATICORED results in the same output folder (we are currently comparing settings...).

Relevant proc part:

# run the regression analysis
3dDeconvolve -input pb03.$subj.r*.volreg+orig.HEAD                            \
    -censor censor_${subj}_combined_2.1D                                      \
    -polort 3 -float                                                          \
    -local_times                                                              \
    -num_stimts 21                                                            \
    -stim_times_AM1 1 stimuli/1_Q_other.txt 'dmBLOCK'                         \
    -stim_label 1 Q_other                                                     \
    -stim_times_AM1 2 stimuli/2_Q_self.txt 'dmBLOCK'                          \
    -stim_label 2 Q_self                                                      \
    -stim_times_AM1 3 stimuli/3_C_other.txt 'dmBLOCK'                         \
    -stim_label 3 C_other                                                     \
    -stim_times_AM1 4 stimuli/4_C_self.txt 'dmBLOCK'                          \
    -stim_label 4 C_self                                                      \
    -stim_times_AM1 5 stimuli/5_O_other_down.txt 'dmBLOCK'                    \
    -stim_label 5 O_other_dwn                                                 \
    -stim_times_AM1 6 stimuli/6_O_other_up.txt 'dmBLOCK'                      \
    -stim_label 6 O_other_up                                                  \
    -stim_times_AM1 7 stimuli/7_O_self_down.txt 'dmBLOCK'                     \
    -stim_label 7 O_self_dwn                                                  \
    -stim_times_AM1 8 stimuli/8_O_self_up.txt 'dmBLOCK'                       \
    -stim_label 8 O_self_up                                                   \
    -stim_times_AM1 9 stimuli/9_motor.txt 'dmBLOCK'                           \
    -stim_label 9 motor                                                       \
    -stim_file 10 motion_demean.1D'[0]' -stim_base 10 -stim_label 10 roll_01  \
    -stim_file 11 motion_demean.1D'[1]' -stim_base 11 -stim_label 11 pitch_01 \
    -stim_file 12 motion_demean.1D'[2]' -stim_base 12 -stim_label 12 yaw_01   \
    -stim_file 13 motion_demean.1D'[3]' -stim_base 13 -stim_label 13 dS_01    \
    -stim_file 14 motion_demean.1D'[4]' -stim_base 14 -stim_label 14 dL_01    \
    -stim_file 15 motion_demean.1D'[5]' -stim_base 15 -stim_label 15 dP_01    \
    -stim_file 16 motion_deriv.1D'[0]' -stim_base 16 -stim_label 16 roll_02   \
    -stim_file 17 motion_deriv.1D'[1]' -stim_base 17 -stim_label 17 pitch_02  \
    -stim_file 18 motion_deriv.1D'[2]' -stim_base 18 -stim_label 18 yaw_02    \
    -stim_file 19 motion_deriv.1D'[3]' -stim_base 19 -stim_label 19 dS_02     \
    -stim_file 20 motion_deriv.1D'[4]' -stim_base 20 -stim_label 20 dL_02     \
    -stim_file 21 motion_deriv.1D'[5]' -stim_base 21 -stim_label 21 dP_02     \
    -allzero_OK                                                               \
    -GOFORIT 6                                                                \
    -fout -tout -x1D X.xmat.1D -xjpeg X.jpg                                   \
    -x1D_uncensored X.nocensor.xmat.1D                                        \
    -fitts fitts.$subj                                                        \
    -errts errts.${subj}                                                      \
    -bucket stats.$subj


# if 3dDeconvolve fails, terminate the script
if ( $status != 0 ) then
    echo '---------------------------------------'
    echo '** 3dDeconvolve error, failing...'
    echo '   (consider the file 3dDeconvolve.err)'
    exit
endif


# display any large pairwise correlations from the X-matrix
1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt

# --------------------------------------------------
# ANATICOR: generate local WMe time series averages
# create catenated volreg dataset
3dTcat -prefix rm.all_runs.volreg pb03.$subj.r*.volreg+orig.HEAD
3dLocalstat -stat mean -nbhd 'SPHERE(45)' -prefix Local_WMe_rall              \
            -mask mask_WMe_resam+orig -use_nonmask                            \
            rm.all_runs.volreg+orig

# -- execute the 3dREMLfit script, written by 3dDeconvolve --
# (include ANATICOR regressors via -dsort)
tcsh -x stats.REML_cmd -dsort Local_WMe_rall+orig

Bonus question: Why is it run in 3dREML.fit? Why is not the ANATICOR part run before the regression and then including these new regressors in the main 3dDeconvolve step? If ANATICOR needs info form the initial regressen, why not run another 3dDeconvolve with the new noise regressors? I Also, I have heard 3dREML is a bit more conservative? Needs some more degrees of freedom?

Thanks!



Edited 6 time(s). Last edit at 10/26/2016 11:27AM by Robin.