Hello AFNI Team,
I'm running into a collinearity issue when running 3dREMLfit. I've pasted the warning message and the 3dDeconvolve + 3dREMLfit commands below.
To look into this, I've checked my timing files and there are no duplicated onsets across my conditions. I've set up the timing files as local times and some runs don't have any onsets. I've added a * for those rows/runs without onsets. I also tried to plot the design matrix made with 3dDeconvolve using 1dplot but it is too big (warning from 3dDeconvolve: + WARNING: Can't plot 3dDecon_rf_aCompCorr_con/rf_matrix.jpg -- matrix size 3912x185 exceeds max=3333). Do you have any guidance on how to troubleshoot this problem?
Thank you -- Catherine
Collinearity warning message from 3dREML
+ X matrix: 19.436% of elements are nonzero
*+ WARNING: -----
*+ WARNING: QR decomposition of [R]^(-1/2) [X] had 5 collinearity problems
*+ WARNING: -----
3dDeconvolve command to make design matrix
3dDeconvolve -input \
${subject}_ses-sen_task-sentences_rec-topup_run-1_space-MNI152NLin2009cAsym_desc-preproc_bold_blur4mm_scaled.nii.gz \
${subject}_ses-sen_task-sentences_rec-topup_run-2_space-MNI152NLin2009cAsym_desc-preproc_bold_blur4mm_scaled.nii.gz \
${subject}_ses-sen_task-sentences_rec-topup_run-3_space-MNI152NLin2009cAsym_desc-preproc_bold_blur4mm_scaled.nii.gz \
${subject}_ses-sen_task-sentences_rec-topup_run-4_space-MNI152NLin2009cAsym_desc-preproc_bold_blur4mm_scaled.nii.gz \
${subject}_ses-sen_task-sentences_rec-topup_run-5_space-MNI152NLin2009cAsym_desc-preproc_bold_blur4mm_scaled.nii.gz \
${subject}_ses-sen_task-sentences_rec-topup_run-6_space-MNI152NLin2009cAsym_desc-preproc_bold_blur4mm_scaled.nii.gz \
-polort A \
-num_stimts 35 \
-mask /usr/local/mridata/Smith_Merit/Processed_Data/derivatives/FMRI_Sentences/Group_Level/tpl-MNI152NLin2009aAsym_res-1_desc-brain_mask_dil2mm_2mm_master.nii.gz \-local_times \
-x1D_stop \
-stim_file 1 confounds/${subject}_rot_x.txt -stim_base 1 -stim_label 1 roll \
-stim_file 2 confounds/${subject}_rot_y.txt -stim_base 2 -stim_label 2 pitch \
-stim_file 3 confounds/${subject}_rot_z.txt -stim_base 3 -stim_label 3 yaw \
-stim_file 4 confounds/${subject}_trans_x.txt -stim_base 4 -stim_label 4 dS \
-stim_file 5 confounds/${subject}_trans_y.txt -stim_base 5 -stim_label 5 dL \
-stim_file 6 confounds/${subject}_trans_z.txt -stim_base 6 -stim_label 6 dP \
-stim_file 7 confounds/${subject}_rot_x_derivative1.txt -stim_base 7 -stim_label 7 rolldx \
-stim_file 8 confounds/${subject}_rot_y_derivative1.txt -stim_base 8 -stim_label 8 pitchdx \
-stim_file 9 confounds/${subject}_rot_z_derivative1.txt -stim_base 9 -stim_label 9 yawdx \
-stim_file 10 confounds/${subject}_trans_x_derivative1.txt -stim_base 10 -stim_label 10 dSdx \
-stim_file 11 confounds/${subject}_trans_y_derivative1.txt -stim_base 11 -stim_label 11 dLdx \
-stim_file 12 confounds/${subject}_trans_z_derivative1.txt -stim_base 12 -stim_label 12 dPdx \
-stim_file 13 confounds/${subject}_rot_x_power2.txt -stim_base 13 -stim_label 13 roll_sq \
-stim_file 14 confounds/${subject}_rot_y_power2.txt -stim_base 14 -stim_label 14 pitch_sq \
-stim_file 15 confounds/${subject}_rot_z_power2.txt -stim_base 15 -stim_label 15 yaw_sq \
-stim_file 16 confounds/${subject}_trans_x_power2.txt -stim_base 16 -stim_label 16 dS_sq \
-stim_file 17 confounds/${subject}_trans_y_power2.txt -stim_base 17 -stim_label 17 dL_sq \
-stim_file 18 confounds/${subject}_trans_z_power2.txt -stim_base 18 -stim_label 18 dP_sq \
-stim_file 19 confounds/${subject}_rot_x_derivative1_power2.txt -stim_base 19 -stim_label 19 rolldx_sq \
-stim_file 20 confounds/${subject}_rot_y_derivative1_power2.txt -stim_base 20 -stim_label 20 pitchdx_sq \
-stim_file 21 confounds/${subject}_rot_z_derivative1_power2.txt -stim_base 21 -stim_label 21 yawdx_sq \
-stim_file 22 confounds/${subject}_trans_x_derivative1_power2.txt -stim_base 22 -stim_label 22 dSdx_sq \
-stim_file 23 confounds/${subject}_trans_y_derivative1_power2.txt -stim_base 23 -stim_label 23 dLdx_sq \
-stim_file 24 confounds/${subject}_trans_z_derivative1_power2.txt -stim_base 24 -stim_label 24 dPdx_sq \
-stim_file 25 confounds/${subject}_a_comp_cor_00.txt -stim_base 25 -stim_label 25 a_comp_cor_00 \
-stim_file 26 confounds/${subject}_a_comp_cor_01.txt -stim_base 26 -stim_label 26 a_comp_cor_01 \
-stim_file 27 confounds/${subject}_a_comp_cor_02.txt -stim_base 27 -stim_label 27 a_comp_cor_02 \
-stim_file 28 confounds/${subject}_a_comp_cor_03.txt -stim_base 28 -stim_label 28 a_comp_cor_03 \
-stim_file 29 confounds/${subject}_a_comp_cor_04.txt -stim_base 29 -stim_label 29 a_comp_cor_04 \
-stim_times 30 /usr/local/mridata/Smith_Merit/Raw_Data/Sentences/Randomization_1/stimes.3567_01_MonthList_sub12.1D 'TENT(0,16,21)' -stim_label 30 month_targets \
-stim_times 31 /usr/local/mridata/Smith_Merit/Raw_Data/Sentences/Randomization_1/stimes.3567_02_WeekList_sub12.1D 'TENT(0,16,21)' -stim_label 31 week_targets \
-stim_times 32 /usr/local/mridata/Smith_Merit/Raw_Data/Sentences/Randomization_1/stimes.3567_03_DayList_sub12.1D 'TENT(0,16,21)' -stim_label 32 day_targets \
-stim_times 33 /usr/local/mridata/Smith_Merit/Raw_Data/Sentences/Randomization_1/stimes.3567_04_HourList_sub12.1D 'TENT(0,16,21)' -stim_label 33 hour_targets \
-stim_times 34 /usr/local/mridata/Smith_Merit/Processed_Data/nifti/${subject}/ses-sen/func/time_files/remember_foils.1D 'TENT(0,16,21)' -stim_label 34 remembered_foils \
-stim_times 35 /usr/local/mridata/Smith_Merit/Processed_Data/nifti/${subject}/ses-sen/func/time_files/forgotten_foils.1D 'TENT(0,16,21)' -stim_label 35 forgotten_foils \
-num_glt 3 \
-gltsym 'SYM: +.5*remembered_foils[8..12] +.5*forgotten_foils[8..12]' \
-glt_label 1 "peak_all_foils" \
-gltsym 'SYM: +remembered_foils[8..12]' \
-glt_label 2 "peak_remembered_foils" \
-gltsym 'SYM: +forgotten_foils[8..12]' \
-glt_label 3 "peak_forgotten_foils" \
-jobs 16 \
-errts 3dDecon_aCompCorr_rf/errts_rf \
-fout -tout -x1D 3dDecon_aCompCorr_rf/rf_matrix.1D -xjpeg 3dDecon_aCompCorr_rf/rf_matrix.jpg \
-bucket 3dDecon_aCompCorr_rf/${subject}_decon_results_rf \
-cbucket 3dDecon_aCompCorr_rf/${subject}_decon_results_rf_cbucket \
3dREMLfit command
3dREMLfit -matrix 3dDecon_rf_aCompCorr_con/rf_matrix.1D \
-input "${subject}_ses-sen_task-sentences_rec-topup_run-1_space-MNI152NLin2009cAsym_desc-preproc_bold_blur4mm_scaled.nii.gz ${subject}_ses-sen_task-sentences_rec-topup_run-2_space-MNI152NLin2009cAsym_desc-preproc_bold_blur4mm_scaled.nii.gz ${subject}_ses-sen_task-sentences_rec-topup_run-3_space-MNI152NLin2009cAsym_desc-preproc_bold_blur4mm_scaled.nii.gz ${subject}_ses-sen_task-sentences_rec-topup_run-4_space-MNI152NLin2009cAsym_desc-preproc_bold_blur4mm_scaled.nii.gz ${subject}_ses-sen_task-sentences_rec-topup_run-5_space-MNI152NLin2009cAsym_desc-preproc_bold_blur4mm_scaled.nii.gz ${subject}_ses-sen_task-sentences_rec-topup_run-6_space-MNI152NLin2009cAsym_desc-preproc_bold_blur4mm_scaled.nii.gz"
-mask /usr/local/mridata/Smith_Merit/Processed_Data/derivatives/FMRI_Sentences/Group_Level/tpl-MNI152NLin2009aAsym_res-1_desc-brain_mask_dil2mm_2mm_master.nii.gz \
-fout -tout -Rbuck 3dDecon_rf_aCompCorr_con/${subject}_decon_results_rf_REML -Rvar 3dDecon_rf_aCompCorr_con/${subject}_decon_results_rf_REMLvar -Rerrts 3dDecon_rf_aCompCorr_con/errts_rf_REML -GOFORIT -verb
