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Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

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The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

History of AFNI updates  

|
March 05, 2021 07:30PM
Hello, AFNI team!

I am trying to run 3dDeconvolve, but I am having trouble with the correct way to specify the basis function. If I use the script below, then I get the message "-'BLOCK' is unknown response function type". If I remove the quotation marks around 'BLOCK(1,6)', then I get the message "Badly placed (."

Please let me know what I am doing wrong and how to do it correctly!

Thank you.

PS There are 6 functional runs and 9 conditions specified by timing files.
----------------
#!/bin/tcsh

foreach subject (313)

#navigate to the 'keep ' directory
cd ${subject}/${subject}.keep

#copy the timing files to this directory
cp ../*.txt ./

#deconvolve here

3dDeconvolve -input pb05.${subject}.r01.scale+tlrc pb05.${subject}.r02.scale+tlrc pb05.${subject}.r03.scale+tlrc pb05.${subject}.r04.scale+tlrc pb05.${subject}.r05.scale+tlrc pb05.${subject}.r06.scale+tlrc -noblock -censor motion_${subject}_censor.1D -ortvec mot_demean.r01.1D mot_demean_r01 -ortvec mot_demean.r02.1D mot_demean_r02 -ortvec mot_demean.r03.1D mot_demean_r03 -ortvec mot_demean.r04.1D mot_demean_r04 -ortvec mot_demean.r05.1D mot_demean_r05 -ortvec mot_demean.r06.1D mot_demean_r06 -polort 2 -num_stimts 9 -stim_times 1 XFC${subject}FarFracFrac.txt -'BLOCK(1,6)' -stim_label 1 farff -stim_times 2 XFC${subject}NearFracFrac.txt -'BLOCK(1,6)' -stim_label 2 nearff -stim_times 3 XFC${subject}MedFracFrac.txt -'BLOCK(1,6)' -stim_label 3 medff -stim_times 4 XFC${subject}FarFracLine.txt -'BLOCK(1,6)' -stim_label 4 farfl -stim_times 5 XFC${subject}NearFracLine.txt -'BLOCK(1,6)' -stim_label 5 nearfl -stim_times 6 XFC${subject}MedFracLine.txt 'BLOCK(1,6)' -stim_label 6 medfl -stim_times 7 XFC${subject}FarLineLine.txt -stim_label 7 farll -stim_times 8 XFC${subject}NearLineLine.txt -stim_label 8 nearll -stim_times 9 XFC${subject}MedLineLine.txt -stim_label 9 medll -gltsym 'SYM: +nearff +nearfl +nearll -farff -farfl -farll' -glt_label 1 all_near_far -gltsym 'SYM: +nearff -farff' -glt_label 2 FF_near_far -gltsym 'SYM: + +nearll -farll' -glt_label 3 LL_near_far -gltsym 'SYM: +nearfl -farfl' -glt_label 4 FL_near_far -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.${subject} -errts errts.${subject} -bucket stats.${subject}

cd ../..

end
Subject Author Posted

3dDeconvolve Question

pkalra2 March 05, 2021 07:30PM

Re: 3dDeconvolve Question

pkalra2 March 05, 2021 07:34PM

Re: 3dDeconvolve Question

pkalra2 March 10, 2021 08:50PM

Re: 3dDeconvolve Question

RWCox March 11, 2021 11:50AM

Re: 3dDeconvolve Question

pkalra2 March 12, 2021 12:58PM

Re: 3dDeconvolve Question

RWCox March 13, 2021 01:33PM

Re: 3dDeconvolve Question

pkalra2 March 15, 2021 06:19PM

Re: 3dDeconvolve Question

RWCox March 15, 2021 08:41PM