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jyaros
October 07, 2019 06:23PM
Hi all, I've already run my proc_py scripts and now want to run a new 3dDeconvolve and 3dREMLFit on my data to get new stats and stats_REML files.

I have a 3dDeconvolve code that works, but cannot figure out how to implement 3dREMLfit in the code. Is there a flag I should be using somewhere?
Here is my code: 

3dDeconvolve -input pb04.${subj}.r01.blur+orig.HEAD pb04.${subj}.r02.blur+orig.HEAD pb04.${subj}.r03.blur+orig.HEAD pb04.${subj}.r04.blur+orig.HEAD \
-mask mask_anat.${subj}+orig -censor censor_${subj}_combined_2.1D -polort 4 -float \
-num_stimts 25 \
-stim_times 1 ${stim_times_dir}SR_remembered.txt 'GAM' -stim_label 1 SR_remembered \
-stim_times 2 ${stim_times_dir}SR_forgotten.txt 'GAM' -stim_label 2 SR_forgotten \
-stim_times 3 ${stim_times_dir}SR_TH.txt 'GAM' -stim_label 3 SR_TH \
-stim_times 4 ${stim_times_dir}SR_TM.txt 'GAM' -stim_label 4 SR_TM \
-stim_times 5 ${stim_times_dir}SR_LCR.txt 'GAM' -stim_label 5 SR_LCR \
-stim_times 6 ${stim_times_dir}SR_LFA.txt 'GAM' -stim_label 6 SR_LFA \
-stim_times 7 ${stim_times_dir}OR_remembered.txt 'GAM' -stim_label 7 OR_remembered \
-stim_times 8 ${stim_times_dir}OR_forgotten.txt 'GAM' -stim_label 8 OR_forgotten \
-stim_times 9 ${stim_times_dir}OR_TH.txt 'GAM' -stim_label 9 OR_TH \
-stim_times 10 ${stim_times_dir}OR_TM.txt 'GAM' -stim_label 10 OR_TM \
-stim_times 11 ${stim_times_dir}OR_LCR.txt 'GAM' -stim_label 11 OR_LCR \
-stim_times 12 ${stim_times_dir}OR_LFA.txt 'GAM' -stim_label 12 OR_LFA \
-stim_times 13 ${stim_times_dir}NoResponse.txt 'GAM' -stim_label 13 NoResponse \
-stim_file 14 'motion_demean.1D[0]' -stim_base 14 -stim_label 14 roll_01 \
-stim_file 15 'motion_demean.1D[1]' -stim_base 15 -stim_label 15 pitch_01 \
-stim_file 16 'motion_demean.1D[2]' -stim_base 16 -stim_label 16 yaw_01 \
-stim_file 17 'motion_demean.1D[3]' -stim_base 17 -stim_label 17 dS_01 \
-stim_file 18 'motion_demean.1D[4]' -stim_base 18 -stim_label 18 dL_01 \
-stim_file 19 'motion_demean.1D[5]' -stim_base 19 -stim_label 19 dP_01 \
-stim_file 20 'motion_deriv.1D[0]' -stim_base 20 -stim_label 20 roll_02 \
-stim_file 21 'motion_deriv.1D[1]' -stim_base 21 -stim_label 21 pitch_02 \
-stim_file 22 'motion_deriv.1D[2]' -stim_base 22 -stim_label 22 yaw_02 \
-stim_file 23 'motion_deriv.1D[3]' -stim_base 23 -stim_label 23 dS_02 \
-stim_file 24 'motion_deriv.1D[4]' -stim_base 24 -stim_label 24 dL_02 \
-stim_file 25 'motion_deriv.1D[5]' -stim_base 25 -stim_label 25 dP_02 \
-iresp 1 iresp_SR_remembered_GAM.${subj} \
-iresp 2 iresp_SR_forgotten_GAM.${subj} \
-iresp 3 iresp_SR_TH_GAM.${subj} \
-iresp 4 iresp_SR_TM_GAM.${subj} \
-iresp 5 iresp_SR_LCR_GAM.${subj} \
-iresp 6 iresp_SR_LFA_GAM.${subj} \
-iresp 7 iresp_OR_remembered_GAM.${subj} \
-iresp 8 iresp_OR_forgotten_GAM.${subj} \
-iresp 9 iresp_OR_TH_GAM.${subj} \
-iresp 10 iresp_OR_TM_GAM.${subj} \
-iresp 11 iresp_OR_LCR_GAM.${subj} \
-iresp 12 iresp_OR_LFA_GAM.${subj} \
-iresp 13 iresp_NoResponse_GAM.${subj} \
-GOFORIT 12 \
-allzero_OK \
-num_glt 1 \
-gltsym 'SYM: +SR_remembered +SR_forgotten +SR_LCR +SR_LFA +SR_TH +SR_TM +OR_remembered +OR_forgotten +OR_LCR +OR_LFA +OR_TH +OR_TM +NoResponse' -glt_label 1 'All Modeled Conditions vs Baseline' \
-jobs $NUM_CPUS \
-fout -tout -x1D X.xmat_GAM.1D -xjpeg X_GAM.jpg \
-x1D_uncensored X.nocensor_GAM.xmat.1D -fitts fitts_GAM.${subj} -errts errts_GAM.${subj} -bucket stats_GAM.${subj} \
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Subject Author Posted

How to run 3dREMLfit on already preprocessed data

jyaros October 07, 2019 06:23PM

Re: How to run 3dREMLfit on already preprocessed data

jyaros October 11, 2019 08:08PM

Re: How to run 3dREMLfit on already preprocessed data

rick reynolds October 12, 2019 12:28PM