AFNI experts,
I am analyzing resting state analysis using the seed-based method. I am interested in looking at executive function network using seed as inferior frontal gyrus. I was able to do everything correctly until proc py using poc py explanation of AFNI. However, I am not sure if the rest of the steps have been done correctly. Could you please check the below scripts and let me know if these have been done okay or if I have missed any?
1. Below was used to extract the seed region from each participant.
#!/bin/tcsh
foreach subj (ls -d /path/subjectID* | sed 's/\// /g' | awk '{print $2}'
)
foreach cond (cond1 cond2)
echo "subj = " ${subj} ", cond = " ${cond}
cd /path/${subj}/${subj}.${cond}/Proc_results
rm -rf EFmask* EF.* EF_* LIFGmask* RIFGmask* Bilat_IFGmask+tlrc Bilat_IFG.ts.1D Bilat_IFG_corr* Bilat_IFG.ts.1D Bilat*
echo “-46 8 26” | 3dUndump -prefix IFGmask1 -srad 5 -master errts.${subj}.${cond}.fanaticor+tlrc -xyz -
echo “46 8 26” | 3dUndump -prefix IFGmask2 -srad 5 -master errts.${subj}.${cond}.fanaticor+tlrc -xyz -
3dcalc -a IFGmask1+tlrc -b IFGmask2+tlrc -expr ‘step(a) + 2*step(b)’ -prefix IFGmask+tlrc
3dmaskave -quiet -mask IFGmask+tlrc. errts.${subj}.${cond}.fanaticor+tlrc > IFG.ts.1D
3dfim+ -bucket IFG_corr -out Correlation -ideal_file IFG.ts.1D -input errts.${subj}.${cond}.fanaticor+tlrc
3dcalc -a IFG_corr+tlrc -exp ‘atanh(a)’ -prefix IFG_r2z
@ linenum++
end
end
2. Below was used to get mean.
#!/bin/tcsh
foreach subj (ls -d /path/subjectID* | sed 's/\// /g' | awk '{print $2}'
)
foreach cond (cond1 cond2)
echo "subj = " ${subj} ", cond = " ${cond}
cd /path/${subj}/${subj}.${cond}/Proc_results
cp IFG_r2z+tlrc.HEAD /path/rsFC_MAPS/IFG_r2z.${subj}.${cond}+tlrc.HEAD
@ linenum++
end
end
3. 3dLME was used to see statistical analysis (group*condition)
#!/bin/sh
3dLME -prefix EF_Sleep
-jobs 4
-model ‘GroupCond’
-ranEff ‘~1’
-SS_type 3
-num_glt 4
-gltLabel 1 ‘AEx-ARest’ -gltCode 1 'Group : 1A Cond : 1Ex -1Rest’
-gltLabel 2 ‘BEx-BRest’ -gltCode 2 ‘Group : 1B Cond : 1Ex -1Rest’
-gltLabel 3 ‘ARest-BRest’ -gltCode 3 'Group : 1A -1B Cond : 1Rest’
-gltLabel 4 ‘AEx-BEx’ -gltCode 4 ‘Group : 1A -1B Cond : 1*Ex’
-mask /path/GM_mask/GM_mask_2009c+tlrc
-dataTable
Subj Group Cond InputFile
AES101 A Ex /path/AES101/AES101.Ex/Proc_results/IFG_r2z+tlrc
AES101 A Rest /path/AES101/AES101.Rest/Proc_results/IFG_r2z+tlrc
AES102 B Ex /path/AES102/AES102.Ex/Proc_results/IFG_r2z+tlrc
AES102 B Rest /path/AES102/AES102.Rest/Proc_results/IFG_r2z+tlrc
AES104 A Ex /path/AES104.Ex/Proc_results/IFG_r2z+tlrc
AES104 A Rest /path/AES104.Rest/Proc_results/IFG_r2z+tlrc
AES107 B Ex /path/AES107/AES107.Ex/Proc_results/IFG_r2z+tlrc
AES107 B Rest /path/AES107/AES107.Rest/Proc_results/IFG_r2z+tlrc \
Thank you in advance for your help!