Hello,

I've been going back and forth on deciding on what 3dDeconvolve options to use for my data, and wanted to see if I could get an expert opinion on the matter (I apologize if this is a lot). What I want to do is select a model that does not assume a canonical HDR model, but instead models with a Finite Impulse Response. It seems to me that CSLPIN will do this, but I wanted to double check.

One issue that I've been running into though is that the length of each stimulus is dependent on subjects' responses, and therefore stimulus presentation for an individual trial can range anywhere from 5-40 sec. Given that one of CSPLIN's parameters is the stimulus offset (stop), would it make sense for me to bin the stim_times timing files such that trials that had similar offset times are passed through 3dDeconvolve together?

Since I'm only interested in the time series of certain ROIs, I've created an ROI mask file where each ROI (32 in total) is given its own value. Would I be able to pass this file (containing all ROIs) through 3dDeconvolve's -mask option, or does the mask have to contain just one ROI at a time?

Given what I've said above, I think I may have an idea of what my 3dDeconvolve command should look like, assuming that the above is reasonably sound:

3dDeconvolve \
-overwrite \
-input $subj.allRuns.pb04.scale_tlrc \
-mask ROIs_all.nii.gz \
-polort A \
-nobout \
-local_times \
-noFDR \
-ortvec ${subj}_all.MoPar_demean.1D demean \
-ortvec ${subj}_all.MoPar_derv.1D derv \
-censor ${subj}_all.censor0.3mm.1D \
-concat '1D: 0 870 1740 2610 3480 4350 5220 6090' \
-num_stimts 2 \
-stim_times 1 $timing_dir/mut.txt 'CSPLIN(0,20,4)' -stim_label 1 mut \
-stim_times 2 $timing_dir/neu.txt 'CSPLIN(0,20,4)' -stim_label 2 neu \
-cbucket ${subj}_Decon_betas.nii.gz \
-bucket ${subj}_Decon.nii.gz \
-xsave \
-x1D ${subj}_xmat.1D \
-fout -tout \
errts ${subj}_errts.nii.gz


Again, thanks for all the help.

Dan



Edited 1 time(s). Last edit at 10/15/2018 01:38PM by Dan.