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myriam.oliver
November 08, 2017 04:00PM
HI!

I am trying to do a correlation analysis from a seed region, but the output does not make sense. I am following the steps in [afni.nimh.nih.gov]

The first error I am facing is in adwarp

$ 3dSynthesize -prefix effectsNoInterest -cbucket all_betas.bil+tlrc -matrix X.xmat.1D -select 0 1 2 4 5 6 7 8 9
++ 3dSynthesize: AFNI version=AFNI_17.0.09 (Feb 10 2017) [64-bit]
++ Authored by: RW Cox
++ Output has 108 time points at TR=2
++ Input had 8 time points censored; filling mode = zero
++ Calculating: ...................................................!
++ Output dataset ./effectsNoInterest+tlrc.BRIK
++ CPU time=0.00 s ; Elapsed=13.16 s

$ 3dcalc -a all_runs.bil+tlrc -b effectsNoInterest+tlrc -expr 'a-b' -prefix CleanData
++ 3dcalc: AFNI version=AFNI_17.0.09 (Feb 10 2017) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./CleanData+tlrc.BRIK

$ adwarp -apar anat_final.bil+tlrc. -dpar CleanData+tlrc -dxyz 3 -prefix EPI_subj_01
++ adwarp: AFNI version=AFNI_17.0.09 (Feb 10 2017) [64-bit]
++ Authored by: R. W. Cox and B. D. Ward
** Error: -apar & -dpar are in same +view!
If this is OK, use -force and -prefix options.

This works if I add the command -force

$ adwarp -apar anat_final.bil+tlrc. -dpar CleanData+tlrc -dxyz 3 -force -prefix EPI_subj_01
++ adwarp: AFNI version=AFNI_17.0.09 (Feb 10 2017) [64-bit]
++ Authored by: R. W. Cox and B. D. Ward
++ Warning: -apar & -dpar are in same +view!
*+ WARNING: Over-writing dataset ./EPI_subj_01+tlrc.HEAD

All the rest of the commands (3dmaskdump/1dtranspose/3dfim+) works perfectly. No errors. But the output of the 3dfim+ (correlation analysis) does not make sense


My input file in 3dSynthesize (called all_betas) contains the information from all participants, while in the example of afni_data6 is just for one. Could be this the problem, that I am choosing the wrong file? However, is the only I get from 3dDeconvolve (see below)

3dDeconvolve -input pb05.$subj.r*.blur+tlrc.HEAD \
-censor motion_${subj}_censor.1D \
-polort 2 \
-num_stimts 7 \
-stim_times 1 shiftedonsets.1D 'BLOCK(24)' \
-stim_label 1 TASK \
-stim_file 2 motion_demean.1D'[0]' -stim_base 2 -stim_label 2 roll \
-stim_file 3 motion_demean.1D'[1]' -stim_base 3 -stim_label 3 pitch \
-stim_file 4 motion_demean.1D'[2]' -stim_base 4 -stim_label 4 yaw \
-stim_file 5 motion_demean.1D'[3]' -stim_base 5 -stim_label 5 dS \
-stim_file 6 motion_demean.1D'[4]' -stim_base 6 -stim_label 6 dL \
-stim_file 7 motion_demean.1D'[5]' -stim_base 7 -stim_label 7 dP \
-jobs 4 -noFDR \
-fout -tout -x1D X.xmat.1D -xjpeg X.jpg \
-x1D_uncensored X.nocensor.xmat.1D \
-fitts fitts.$subj \
-errts errts.$subj \
-cbucket all_betas.$subj \
-bucket stats.$subj \
-bout.

Thanks so much!
Myriam
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Correlation analysis from seed

myriam.oliver November 08, 2017 04:00PM