Hello,

I'm wondering if it would be reasonable or beneficial to take the output of -Rerrts output from 3dREMLfit and use it in 3ddeconvolve. I pasted an example script below. What are your thoughts?


3dDeconvolve -input ./$subject.ALL.PP.TAL.PY+tlrc -num_stimts 6 -x1D {$subject}.NoMotion_S.xmat.1D -x1D_stop \
-stim_file 1 ./${subject}.ALL_motion.1D'['0']' -stim_base 1 -stim_label 1 pitch \
-stim_file 2 ./${subject}.ALL_motion.1D'['1']' -stim_base 2 -stim_label 2 roll \
-stim_file 3 ./${subject}.ALL_motion.1D'['2']' -stim_base 3 -stim_label 3 yaw \
-stim_file 4 ./${subject}.ALL_motion.1D'['3']' -stim_base 4 -stim_label 4 dx \
-stim_file 5 ./${subject}.ALL_motion.1D'['4']' -stim_base 5 -stim_label 5 dy \
-stim_file 6 ./${subject}.ALL_motion.1D'['5']' -stim_base 6 -stim_label 6 dz \
-concat ./ConcatCuts.1D -polort 'A'

3dREMLfit -matrix ./${subject}.NoMotion_S.xmat.1D \
-input ./${subject}.ALL.PP.TAL.PY+tlrc -tout\
-Rvar ./${subject}.NoMotion_REMLvar \
-Rerrts ./${subject}.NoMotionErrTs_REML

3dDeconvolve -input $subject.NoMotionErrTs_REML+tlrc -num_stimts 9 \
-stim_file 1 ./${subject}.ALL_motion.1D'['0']' -stim_base 1 -stim_nptr 1 1 -stim_label 1 pitch \
-stim_file 2 ./${subject}.ALL_motion.1D'['1']' -stim_base 2 -stim_nptr 2 1 -stim_label 2 roll \
-stim_file 3 ./${subject}.ALL_motion.1D'['2']' -stim_base 3 -stim_nptr 3 1 -stim_label 3 yaw \
-stim_file 4 ./${subject}.ALL_motion.1D'['3']' -stim_base 4 -stim_nptr 4 1 -stim_label 4 dx \
-stim_file 5 ./${subject}.ALL_motion.1D'['4']' -stim_base 5 -stim_nptr 5 1 -stim_label 5 dy \
-stim_file 6 ./${subject}.ALL_motion.1D'['5']' -stim_base 6 -stim_nptr 6 1 -stim_label 6 dz \
-local_times -stim_times 7 ./$subject.Con_S.1D 'BLOCK5(1,1)' -stim_label 7 Constant \
-local_times -stim_times 8 ./$subject.ME_S.1D 'BLOCK5(1,1)' -stim_label 8 ME \
-local_times -stim_times_AM2 9 ./$subject.MagAMcat_S.1D 'BLOCK5(1,1)' -stim_label 9 Mag \
-concat ./ConcatCuts.1D -jobs 10 \
-bucket {$subject}.DelAdjMag \
-tout -fout -polort 'A'