Hello AFNI experts,

I have been having an issue where I am getting % signal change values in the thousands from 3dROIstats for the extracted clusters for some subjects in one of my conditions, and I cannot seem to figure out why this may be (clearly these values are incorrect). It is odd because I do not have this problem for the majority of my subjects who were run on the exact same scripts, and this problem only occurs for 1 of the 2 conditions, even though both conditions were run through the same code for all subjects. I have searched through the AFNI message boards and run google searches to see if anyone else has had this issue, and I was not finding any luck there.

Do you have any idea what might be causing this problem?

I have copied and pasted all of the code for 1 of these problem subjects below. The condition we are having issues with is the data in the Imagery Condition for the Trauma imagery (not the neutral imagery).

#Preprocessing of IRC PTSD grant FACES and IMAGERY task data.
#Reconstruction of functional and anatomical data

#sets folder containing data
setenv subfolder /Users/Studies/IRC_PTSD/Data

#Creates a variable named "study", and sets the value.
set study = IRCPTSD

#Prints the value of the variables to terminal - check it!
echo $study

#RECONSTRUCTION - ANATOMICAL DATA
#WILL NEED TO ENTER CORRECT SUBJECT IN LIST
foreach subject (sub1120)
cd ${subfolder}/${subject}

to3d -prefix ${subject}.${study}.spgr spgr/i*
end

#RECONSTRUCTION - FUNCTIONAL DATA - FACES
#WRITE DOWN SUB-BRIKS WITH OUTLIERS
#-time:zt numslices numTRs TR order of acquistion
# TRs = 18 blocks * 18 s per block (9 TRs) + 3 TRs at beginning + 2 TRs at #end because of slow presentation for faces 1 observed by Chris = 167

foreach subject (sub1120)
foreach condition (faces1 faces2)

to3d -prefix ${subject}.${study}.${condition} -save_outliers ${subject}.${study}.${condition}_out.txt \
-time:zt 38 167 2s alt+z ${condition}/i*
end
end

#RECONSTRUCTION - FUNCTIONAL DATA - IMAGERY
#WRITE DOWN SUB-BRIKS WITH OUTLIERS
# TRs = 3 minutes per imagery trial (90 TRs) * 3 imagery trials + 3 TRs at beginning = 273

foreach subject (sub1120)
foreach condition (neutral_im trauma_im)

to3d -prefix ${subject}.${study}.${condition} -save_outliers ${subject}.${study}.${condition}_out.txt \
-time:zt 38 273 2s alt+z ${condition}/'i*'

end
end


#RECONSTRUCTION - FUNCTIONAL DATA - RESTING
#WRITE DOWN SUB-BRIKS WITH OUTLIERS
# TRs = 180 TRs (6 min)

foreach subject (sub1120)
to3d -prefix ${subject}.${study}.resting -save_outliers ${subject}.${study}.resting_out.txt \
-time:zt 38 180 2s alt+z resting/i*
end

#Preprocessing of IRC PTSD grant FACES and IMAGERY task data.
#Talairach transforms the anatomical.
#spatial registration, spatial filter, brain mask

#sets folder containing data
setenv subfolder /Users/Studies/IRC_PTSD/Data

#Creates a variable named "study", and sets the value.
set study = IRCPTSD

#Prints the value of the variables to terminal - check it!
echo $study

#ALIGNS THE FUNCTIONAL TO THE ANATOMICAL
#YOU WILL NEED TO CHANGE EPI BASE TO THE SCRIPT RUN IMMEDIATELY AFTER SPGR COLLECTED AND THEN MATCH CHOSEN EPI sub-brik BASELINE NUMBER

foreach subject (sub1120)

cd ${subfolder}/${subject}

#FIND MEAN VALUE OF TIMESERIES FOR NORMALIZATION
foreach subject (sub1120)
foreach condition ( faces1 faces2 neutral_im trauma_im resting )
3dTstat -mean -prefix ${subject}.${study}.${condition}_mean_NoBlur \
${subject}.${study}.${condition}_al+orig
end
end


#CREATE A MASK OF BRAIN VOXELS (concatenates first)
#Voxels outside of brain will be set to zero
#NEED TO CHANGE DEPENDING ON NUMBER OF RUNS
#concatenation of all 2 runs - just for convenience

foreach subject (sub1120)
3dTcat -prefix ${subject}.${study}_rall_al_NoBlur \
${subject}.${study}.faces1_al+orig \
${subject}.${study}.faces2_al+orig \
${subject}.${study}.neutral_im_al+orig \
${subject}.${study}.trauma_im_al+orig
end

#create a mask to distinguish brain from non-brain voxels
foreach subject (sub1120)
3dAutomask -clfrac .20 -nbhrs 14 -peels 0 -prefix ${subject}.${study}_mask_NoBlur \
${subject}.${study}_rall_al_NoBlur+orig
end

#CALCULATES SNR BY DIVIDING EACH VOXEL'S MEAN BY IT'S SD

foreach subject (sub1120)
foreach condition ( faces1 faces2 neutral_im trauma_im resting )
3dTstat -stdev -prefix ${subject}.${study}.${condition}_stdev_NoBlur \
${subject}.${study}.${condition}_al+orig
end
end

foreach subject (sub1120)
foreach condition ( faces1 faces2 neutral_im trauma_im resting )
3dcalc -fscale -a ${subject}.${study}.${condition}_mean_NoBlur+orig \
-b ${subject}.${study}.${condition}_stdev_NoBlur+orig \
-expr "a/b" \
-prefix ${subject}.${study}.${condition}_SNR_NoBlur
end
end

#Preprocessing of IRC PTSD grant FACES and IMAGERY task data.
#Normalizatrion to % signal change, concatenation & single subject deconvolution.

#sets folder containing data
setenv subfolder /Users/Studies/IRC_PTSD/Data

#Creates a variable named "study", and sets the value.
set study = IRCPTSD

#Prints the value of the variables to terminal - check it!
echo $study

#NORMALIZE THE TIMESERIES IN EACH VOXEDL TO MEAN OF 100
#this will make your final regression coefficients expressed as percent #signal change

foreach subject (sub463 sub418 sub305 sub275 sub116 sub1120)
cd ${subfolder}/${subject}

foreach condition ( faces1 faces2 neutral_im trauma_im resting )
3dcalc -fscale -a ${subject}.${study}.${condition}_al+orig \
-b ${subject}.${study}.${condition}_mean_NoBlur+orig -c ${subject}.${study}_mask_NoBlur+orig \
-expr "c*(a/b*100)" -prefix ${subject}.${study}.${condition}_scaled_NoBlur
end

#DETREND????

#CONCATENATE RUNS - FACES
#puts all runs together. We'll also drop the first 3 images (due to #baseline issues)
#NEED TO CHANGE IF USED DIFFERENT NUMBER OF BASELINE IMAGES
3dTcat -prefix ${subject}.${study}.rall.face_scaled_NoBlur \
${subject}.${study}.faces1_scaled_NoBlur+orig"[3..166]" \
${subject}.${study}.faces2_scaled_NoBlur+orig"[3..166]"

#CONCATENATE RUNS - IMAGERY
#puts all runs together. We'll also drop the first 3 images (due to #baseline issues)
#NEED TO CHANGE IF USED DIFFERENT NUMBER OF BASELINE IMAGES
3dTcat -prefix ${subject}.${study}.rall.imagery_scaled_NoBlur \
${subject}.${study}.neutral_im_scaled_NoBlur+orig"[3..272]" \
${subject}.${study}.trauma_im_scaled_NoBlur+orig"[3..272]"


#SINGLE SUBJECT REGRESSION ANALYSIS - FACE
3dDeconvolve -xout -input {$subject}.${study}.rall.face_scaled_NoBlur+orig \
-censor ${subject}.${study}.faces_outliers.1D \
-polort 3 \
-num_stimts 3 \
-stim_file 1 /Users/Studies/IRC_PTSD/Scripts/happy.1D -stim_label 1 happy \
-stim_file 2 /Users/Studies/IRC_PTSD/Scripts/neutral.1D -stim_label 2 neutral \
-stim_file 3 /Users/Studies/IRC_PTSD/Scripts/fear.1D -stim_label 3 fear \
-concat /Users/Studies/IRC_PTSD/Scripts/face.concat \
-num_glt 3 \
-gltsym 'SYM: +happy -neutral' -glt_label 1 happy_vs_neutral \
-gltsym 'SYM: +fear -neutral' -glt_label 2 fear_vs_neutral \
-gltsym 'SYM: +happy -fear' -glt_label 3 happy_vs_fear \
-full_first -fout -tout -bout \
-fitts ${subject}.${study}.face_func_MRfitts_NoBlur \
-bucket ${subject}.${study}.face_func_MR_NoBlur \
-errts ${subject}.${study}.face_rts_NoBlur

3dFWHMx -dset ${subject}.${study}.face_rts_NoBlur+orig -mask ${subject}.${study}_mask_NoBlur+orig -out \
${subject}.${study}.face_fwhm_NoBlur.txt


#SINGLE SUBJECT REGRESSION ANALYSIS - IMAGERY
# 8 conditions: baseline, script, recall, rest for both trauma & neutral
3dDeconvolve -xout -input {$subject}.${study}.rall.imagery_scaled_NoBlur+orig \
-censor ${subject}.${study}.imagery_outliers.1D \
-GOFORIT 1 \
-polort 4 \
-num_stimts 8 \
-stim_file 1 /Users/Studies/IRC_PTSD/Scripts/im_neut_base.1D -stim_label 1 im_neut_base \
-stim_file 2 /Users/Studies/IRC_PTSD/Scripts/im_neut_script.1D -stim_label 2 im_neut_script \
-stim_file 3 /Users/Studies/IRC_PTSD/Scripts/im_neut_recall.1D -stim_label 3 im_neut_recall \
-stim_file 4 /Users/Studies/IRC_PTSD/Scripts/im_neut_rest.1D -stim_label 4 im_neut_rest \
-stim_file 5 /Users/Studies/IRC_PTSD/Scripts/im_trauma_base.1D -stim_label 5 im_trauma_base \
-stim_file 6 /Users/Studies/IRC_PTSD/Scripts/im_trauma_script.1D -stim_label 6 im_trauma_script \
-stim_file 7 /Users/Studies/IRC_PTSD/Scripts/im_trauma_recall.1D -stim_label 7 im_trauma_recall \
-stim_file 8 /Users/Studies/IRC_PTSD/Scripts/im_trauma_rest.1D -stim_label 8 im_trauma_rest \
-concat /Users/Studies/IRC_PTSD/Scripts/imagery.concat \
-num_glt 8 \
-gltsym 'SYM: +im_neut_recall -im_neut_base' -glt_label 1 im_neutrecall_vs_base \
-gltsym 'SYM: +im_trauma_recall -im_trauma_base' -glt_label 2 im_traumarecall_vs_base \
-gltsym 'SYM: +im_neut_rest -im_neut_base' -glt_label 3 im_neutrest_vs_base \
-gltsym 'SYM: +im_trauma_rest -im_trauma_base' -glt_label 4 im_traumarest_vs_base \
-gltsym 'SYM: +im_trauma_recall -im_neut_recall' -glt_label 5 im_traumarecall_vs_neutrecall \
-gltsym 'SYM: +im_trauma_rest -im_neut_rest' -glt_label 6 im_traumarest_vs_neutrest \
-gltsym 'SYM: +im_trauma_script -im_neut_script' -glt_label 7 im_traumascript_vs_neutscript \
-gltsym 'SYM: +im_trauma_base -im_neut_base' -glt_label 8 im_traumabase_vs_neutbase \
-full_first -fout -tout -bout \
-fitts ${subject}.${study}.imagery_func_MRfitts_NoBlur \
-bucket ${subject}.${study}.imagery_func_MR_NoBlur \
-errts ${subject}.${study}.imagery_rts_NoBlur

3dFWHMx -dset ${subject}.${study}.imagery_rts_NoBlur+orig -mask ${subject}.${study}_mask_NoBlur+orig \
-out ${subject}.${study}.imagery_fwhm_NoBlur.txt

end

#Preprocessing of IRC PTSD grant FACES task data.
#Talairach transforms the functional data - MUST HAVE TALAIRACHED STRUCTURAL IMAGE FIRST!!!!

#sets folder containing data
setenv subfolder /Users/Studies/IRC_PTSD/Data
setenv facefolder /Users/Studies/IRC_PTSD/Data/facegroupdata
setenv imageryfolder /Users/Studies/IRC_PTSD/Data/imagerygroupdata

#Creates a variable named "study", and sets the value.
set study = IRCPTSD

#Prints the value of the variables to terminal - check it!
echo $study

foreach subject (sub1120)
cd ${subfolder}/${subject}

#APPLY SPATIAL FILTER
#MAY WANT TO CHANGE FILTER SIZE
3dmerge -doall -1blur_fwhm 6 -prefix ${subject}.${study}.face_func_MR_Blurred \
${subject}.${study}.face_func_MR_NoBlur+orig

3dmerge -doall -1blur_fwhm 6 -prefix ${subject}.${study}.imagery_func_MR_Blurred \
${subject}.${study}.imagery_func_MR_NoBlur+orig


#TALAIRACH TRANSFORMS FUNCTIONAL DATA - FACES

adwarp -apar ${subject}.${study}.spgr+tlrc -dpar ${subject}.${study}.face_func_MR_Blurred+orig'[17]' \
-prefix ${facefolder}/${subject}.${study}_happy_ReBlurred
adwarp -apar ${subject}.${study}.spgr+tlrc -dpar ${subject}.${study}.face_func_MR_Blurred+orig'[20]' \
-prefix ${facefolder}/${subject}.${study}_neutral_ReBlurred
adwarp -apar ${subject}.${study}.spgr+tlrc -dpar ${subject}.${study}.face_func_MR_Blurred+orig'[23]' \
-prefix ${facefolder}/${subject}.${study}_fear_ReBlurred


#talairach transform functional data - IMAGERY.

adwarp -apar ${subject}.${study}.spgr+tlrc -dpar ${subject}.${study}.imagery_func_MR_Blurred+orig'[21]' \
-prefix ${imageryfolder}/${subject}.${study}_im_neut_base_ReBlurred
adwarp -apar ${subject}.${study}.spgr+tlrc -dpar ${subject}.${study}.imagery_func_MR_Blurred+orig'[24]' \
-prefix ${imageryfolder}/${subject}.${study}_im_neut_script_ReBlurred
adwarp -apar ${subject}.${study}.spgr+tlrc -dpar ${subject}.${study}.imagery_func_MR_Blurred+orig'[27]' \
-prefix ${imageryfolder}/${subject}.${study}_im_neut_recall_ReBlurred
adwarp -apar ${subject}.${study}.spgr+tlrc -dpar ${subject}.${study}.imagery_func_MR_Blurred+orig'[30]' \
-prefix ${imageryfolder}/${subject}.${study}_im_neut_rest_ReBlurred
adwarp -apar ${subject}.${study}.spgr+tlrc -dpar ${subject}.${study}.imagery_func_MR_Blurred+orig'[33]' \
-prefix ${imageryfolder}/${subject}.${study}_im_trauma_base_ReBlurred
adwarp -apar ${subject}.${study}.spgr+tlrc -dpar ${subject}.${study}.imagery_func_MR_Blurred+orig'[36]' \
-prefix ${imageryfolder}/${subject}.${study}_im_trauma_script_ReBlurred
adwarp -apar ${subject}.${study}.spgr+tlrc -dpar ${subject}.${study}.imagery_func_MR_Blurred+orig'[39]' \
-prefix ${imageryfolder}/${subject}.${study}_im_trauma_recall_ReBlurred
adwarp -apar ${subject}.${study}.spgr+tlrc -dpar ${subject}.${study}.imagery_func_MR_Blurred+orig'[42]' \
-prefix ${imageryfolder}/${subject}.${study}_im_trauma_rest_ReBlurred


#RESAMPLES THE DATA BACK TO ORIGINAL VOXEL SIZE TO SPEED UP CALCULATIONS - FACES
foreach valence (happy fear neutral)
3dresample -dxyz 3.75 3.75 3.7 -rmode 'NN' -inset ${facefolder}/${subject}.${study}_${valence}_ReBlurred+tlrc \
-prefix ${facefolder}/${subject}.${study}_${valence}_ReBlurred_rs+tlrc
end

#RESAMPLES THE DATA BACK TO ORIGINAL VOXEL SIZE TO SPEED UP CALCULATIONS - FACES
foreach valence (im_neut_base im_neut_script im_neut_recall im_neut_rest im_trauma_base im_trauma_script im_trauma_recall im_trauma_rest)
3dresample -dxyz 3.75 3.75 3.7 -rmode 'NN' -inset ${imageryfolder}/${subject}.${study}_${valence}_ReBlurred+tlrc \
-prefix ${imageryfolder}/${subject}.${study}_${valence}_ReBlurred_rs+tlrc
end

Next we created a group mask for AlphaSim, ran AlphaSim, and created masks for surviving clusters below:

#Creates a variable called "sufolder" for the folder location where the data is kept.
setenv subfolder /Users/studies/IRC_PTSD/Data/imagerygroupdata

#Creates a variable named "study" and sets the value.
set study = IRCPTSD

#Creates clusters based on 1630 cubic mm with a radius of 1.
#NEED TO INSERT THE PROPER F-VALUE FROM CLUSTERING AFTER -1THRESH (is currently 4.444)
3dmerge -1clust 1 1630 -1thresh 4.444 -prefix Imagery_Script_GroupxValence_clust+tlrc Script_Imagery_ANOVA+tlrc'[5]'

Same as above but assigns numbers to clusters
#NEED TO INSERT PROPER F-VALUE FROM CLUSTERING AFTER -1THRESH (is currently 4.444)
3dmerge -1clust_order 1 1630 -1thresh 4.444 -prefix Imagery_Script_GroupxValence_clust_order+tlrc Script_Imagery_ANOVA+tlrc'[5]'

foreach subject (sub2325)
3dROIstats -nzmean -mask Imagery_Script_GroupxValence_clust_order+tlrc ${subject}.${study}_im_trauma_script_ReBlurred+tlrc \
>>${subject}.${study}_im_trauma_script_ReBlurred_GroupxValence_ftest.txt

3dROIstats -nzmean -mask Imagery_Script_GroupxValence_clust_order+tlrc ${subject}.${study}_im_neut_script_ReBlurred+tlrc \
>>${subject}.${study}_im_neut_script_ReBlurred_GroupxValence_ftest.txt
end


Any suggestions as to what the issue might be would be great.

Thanks!!

Lauren