Re-opening this topic because I have run into same high correlation issues mentioned previously (New results image at bottom). Note: We have swapped over to the recommended Beta-series estimation approach (Thanks Gang for patience and recommendations there). Now looking for assistance trying to sort out where these excessively high correlations are still coming from. Included below are scripts that could involve motion regression, since Daniel mentioned earlier in this thread that this is most common place these issues arise. Open to other ideas and happy to include scripts where helpful.

Current process is as follows:

1. Activation analysis using 3dDeconvolve(1st time) with Stim_times_AM1, Dmblock, motion, and censoring
2. 3dTtest++ with ClustSim for group analysis of conditions and selection of high activitation ROIs (all activation output as expected and normal signif levels)
3. BetaSeries estimation using 3dDeconvolve(2nd time) with polort 1, stim_times_IM, dmblock, motion, and censoring (see Step #3 script below)
4. 3dBucket to select relevant trials/subriks from desired condition
5. 3drefit to change into 3dtime dataset
6. 3dMaskave to pull relevant .1D ROI timeseries
7. 1d_tool.py and 3dTstat+3dCalc to demean both .1D ROI time series and whole brain volume (as recommended by Colm in this thread * Note correlation area same with and without step
8. Seed to Whole-brain Correlation analysis via 3dDeconvolve (3rd time) with stim_file1, no censoring, no motion, and polort 0...(as recommended by gang in this thread (see Step #8 script below)
9. 3dCalc to change R^2 to R
10. 3dCalc for R-to-Z transform
11. 3dTtest++ again with ClustSim to assess across subjects.

12**. I have also run this using 3dfim+ and last 2 steps as a sanity check. Unfortunately that also has same hugely high correlation values.

Assistance and ideas much appreciated since I know this has to be user error somewhere.

~Dane

-------------------------------------------------------
Step #3 script
3dDeconvolve \
-jobs 4 \
-force_TR 2.5 \
-input ${subj}_prepro_all+tlrc \
-mask ${subj}_s4_vr_zp4_cardnudg_e2a_amsk+tlrc \
-censor $censorfile/${subj}_autocensor_AC3VC_pre-moco.1D \
-nfirst 0 \
-polort 1 \
-allzero_OK \
-GOFORIT 3 \
-local_times \
-basis_normall 1 \
-num_stimts 9 \
-stim_times_IM 1 $stimdir/${subj}_Strong_stim5c_p3.4.1D 'dmBLOCK(1)' -stim_label 1 'StrgBeta' \
-stim_times_IM 2 $stimdir/${subj}_Weak_stim5c_p3.4.1D 'dmBLOCK(1)' -stim_label 2 'WeakBeta' \
-stim_times_IM 3 $stimdir/${subj}_Silence_stim5c_p3.4.1D 'dmBLOCK(1)' -stim_label 3 'SlncBeta' \
-stim_file 4 $motiondir/${subj}_motion_all.1D'[0]' -stim_label 4 'roll' \
-stim_file 5 $motiondir/${subj}_motion_all.1D'[1]' -stim_label 5 'pitch' \
-stim_file 6 $motiondir/${subj}_motion_all.1D'[2]' -stim_label 6 'yaw' \
-stim_file 7 $motiondir/${subj}_motion_all.1D'[3]' -stim_label 7 'dS' \
-stim_file 8 $motiondir/${subj}_motion_all.1D'[4]' -stim_label 8 'dL' \
-stim_file 9 $motiondir/${subj}_motion_all.1D'[5]' -stim_label 9 'dP' \
-stim_base 4 -stim_base 5 -stim_base 6 -stim_base 7 -stim_base 8 -stim_base 9 \
-x1D $outputdir/${subj}/${subj}_activationP1_S3_Q2_st5c_p34_dmbIM.xmat.1D -xjpeg \
$outputdir/${subj}/${subj}_activationP1_S3_Q2_st5c_p34_dmbIM.jpg \
-bucket $outputdir/${subj}/${subj}_activationP1_S3_Q2_st5c_p34_dmbIM_Bucket \


Step #8 Script
3dDeconvolve \
-force_TR 2.5 \
-input $subjectsdir/${subj}/${subj}_activationP1_S3_Q2_st5c_P34_dmbIM_StrgBetas_MAPdemean+tlrc \
-polort 0 \
-mask ${subj}_s4_vr_zp4_cardnudg_e2a_amsk+tlrc. \
-GOFORIT 3 \
-local_times \
-num_stimts 1 \
-stim_file 1 $subjectsdir/${subj}/${subj}_activationP1_S3_Q2_st5c_P34_dmbIM_StrgBetas_MAP_${ROI}_Timeseries_demean.1D \
-stim_label 1 StrgBeta_demSeed_${ROI} \
-rout \
-fout \
-bucket $subjectsdir/${subj}/${subj}_activationP1_S3_Q2_st5c_P34_dmbIM_StrgBetas_MAPdemean_${ROI}_roi2wb_r^2map \



Edited 1 time(s). Last edit at 08/31/2022 08:44PM by daanderson.