Hello Gang et al.
I am running a rather simple within subjects LMM on resting state fMRI scans of 50 subjects who experienced 2 different scans, which I label 'states'.

When I attempt to use 3dmerge to extract the mean state-dependent functional connectivity maps from the gltCode (using, e.g : 3dmerge -1clust 3 54 -1thresh 7.14 -1erode 50 -1dilate -prefix newfilenamep10-12 ‘outputfilefrom3dlmer+tlrc[4]’)

The Z-stats in the 4th subbrik are astronomical (z-stat 7.14 corresponds to a threshold of p = 1x10^-12) and the maps still cover quite a lot of the brain at this level. The thresholded maps are attached for reference (seed-driven FC from the left amygdala for each state).

1. Are these statistics valid? Even between states within the same participants within the same scanning session, the appearance of a difference is very dramatic.
2. How would I arrive at a rational statistical threshold for the mean functional connecitivity maps? the p-value of these maps is 1x10^-12 and the cluster extent is 54 mm^3 (2 voxels in real space).
3. or did I make a serious mistake somewhere?

Thank you.

Tim Meeker

The full model specification is below:


for seed in bilataMCC #bilatpgACC bilatsgACC bilatspgACC PAGanat
do

3dLMEr -prefix Capsaicin${seed}gm -jobs 8 \
-mask /data/tim/DPMN2019/gncREST_groupmask+tlrc \
-model 'state+(1|Subj)' \
-gltCode control 'state : 1*control' \
-gltCode pain 'state : 1*pain' \
-gltCode pain-control 'state : 1*pain -1*control' \
-dataTable \
Subj state InputFile \
s1 control /data/tim/DPMN2019/1stlevel/${seed}gnc1007REST1Z_gm+tlrc \
s1 pain /data/tim/DPMN2019/1stlevel/${seed}gnc1007REST2Z_gm+tlrc \
s2 control /data/tim/DPMN2019/1stlevel/${seed}gnc1022REST1Z_gm+tlrc \
s2 pain /data/tim/DPMN2019/1stlevel/${seed}gnc1022REST2Z_gm+tlrc \
s3 control /data/tim/DPMN2019/1stlevel/${seed}gnc1048REST1Z_gm+tlrc \
s3 pain /data/tim/DPMN2019/1stlevel/${seed}gnc1048REST2Z_gm+tlrc \
s4 control /data/tim/DPMN2019/1stlevel/${seed}gnc1054REST1Z_gm+tlrc \
s4 pain /data/tim/DPMN2019/1stlevel/${seed}gnc1054REST2Z_gm+tlrc \
s5 control /data/tim/DPMN2019/1stlevel/${seed}gnc1060REST1Z_gm+tlrc \
s5 pain /data/tim/DPMN2019/1stlevel/${seed}gnc1060REST2Z_gm+tlrc \
s6 control /data/tim/DPMN2019/1stlevel/${seed}gnc1062REST1Z_gm+tlrc \
s6 pain /data/tim/DPMN2019/1stlevel/${seed}gnc1062REST2Z_gm+tlrc \
s7 control /data/tim/DPMN2019/1stlevel/${seed}gnc1088REST1Z_gm+tlrc \
s7 pain /data/tim/DPMN2019/1stlevel/${seed}gnc1088REST2Z_gm+tlrc \
s8 control /data/tim/DPMN2019/1stlevel/${seed}gnc2003REST1Z_gm+tlrc \
s8 pain /data/tim/DPMN2019/1stlevel/${seed}gnc2003REST2Z_gm+tlrc \
s9 control /data/tim/DPMN2019/1stlevel/${seed}gnc2005REST1Z_gm+tlrc \
s9 pain /data/tim/DPMN2019/1stlevel/${seed}gnc2005REST2Z_gm+tlrc \
s10 control /data/tim/DPMN2019/1stlevel/${seed}gnc2017REST1Z_gm+tlrc \
s10 pain /data/tim/DPMN2019/1stlevel/${seed}gnc2017REST2Z_gm+tlrc \
s11 control /data/tim/DPMN2019/1stlevel/${seed}gnc2029REST1Z_gm+tlrc \
s11 pain /data/tim/DPMN2019/1stlevel/${seed}gnc2029REST2Z_gm+tlrc \
s12 control /data/tim/DPMN2019/1stlevel/${seed}gnc2032REST1Z_gm+tlrc \
s12 pain /data/tim/DPMN2019/1stlevel/${seed}gnc2032REST2Z_gm+tlrc \
s13 control /data/tim/DPMN2019/1stlevel/${seed}gnc2044REST1Z_gm+tlrc \
s13 pain /data/tim/DPMN2019/1stlevel/${seed}gnc2044REST2Z_gm+tlrc \
s14 control /data/tim/DPMN2019/1stlevel/${seed}gnc2053REST1Z_gm+tlrc \
s14 pain /data/tim/DPMN2019/1stlevel/${seed}gnc2053REST2Z_gm+tlrc \
s15 control /data/tim/DPMN2019/1stlevel/${seed}gnc2056REST1Z_gm+tlrc \
s15 pain /data/tim/DPMN2019/1stlevel/${seed}gnc2056REST2Z_gm+tlrc \
s16 control /data/tim/DPMN2019/1stlevel/${seed}gnc2057REST1Z_gm+tlrc \
s16 pain /data/tim/DPMN2019/1stlevel/${seed}gnc2057REST2Z_gm+tlrc \
s17 control /data/tim/DPMN2019/1stlevel/${seed}gnc2058REST1Z_gm+tlrc \
s17 pain /data/tim/DPMN2019/1stlevel/${seed}gnc2058REST2Z_gm+tlrc \
s18 control /data/tim/DPMN2019/1stlevel/${seed}gnc2063REST1Z_gm+tlrc \
s18 pain /data/tim/DPMN2019/1stlevel/${seed}gnc2063REST2Z_gm+tlrc \
s19 control /data/tim/DPMN2019/1stlevel/${seed}gnc2065REST1Z_gm+tlrc \
s19 pain /data/tim/DPMN2019/1stlevel/${seed}gnc2065REST2Z_gm+tlrc \
s20 control /data/tim/DPMN2019/1stlevel/${seed}gnc2066REST1Z_gm+tlrc \
s20 pain /data/tim/DPMN2019/1stlevel/${seed}gnc2066REST2Z_gm+tlrc \
s21 control /data/tim/DPMN2019/1stlevel/${seed}gnc2071REST1Z_gm+tlrc \
s21 pain /data/tim/DPMN2019/1stlevel/${seed}gnc2071REST2Z_gm+tlrc \
s22 control /data/tim/DPMN2019/1stlevel/${seed}gnc2072REST1Z_gm+tlrc \
s22 pain /data/tim/DPMN2019/1stlevel/${seed}gnc2072REST2Z_gm+tlrc \
s23 control /data/tim/DPMN2019/1stlevel/${seed}gnc2074REST1Z_gm+tlrc \
s23 pain /data/tim/DPMN2019/1stlevel/${seed}gnc2074REST2Z_gm+tlrc \
s24 control /data/tim/DPMN2019/1stlevel/${seed}gnc2075REST1Z_gm+tlrc \
s24 pain /data/tim/DPMN2019/1stlevel/${seed}gnc2075REST2Z_gm+tlrc \
s25 control /data/tim/DPMN2019/1stlevel/${seed}gnc2077REST1Z_gm+tlrc \
s25 pain /data/tim/DPMN2019/1stlevel/${seed}gnc2077REST2Z_gm+tlrc \
s26 control /data/tim/DPMN2019/1stlevel/${seed}gnc2079REST1Z_gm+tlrc \
s26 pain /data/tim/DPMN2019/1stlevel/${seed}gnc2079REST2Z_gm+tlrc \
s27 control /data/tim/DPMN2019/1stlevel/${seed}gnc2083REST1Z_gm+tlrc \
s27 pain /data/tim/DPMN2019/1stlevel/${seed}gnc2083REST2Z_gm+tlrc \
s28 control /data/tim/DPMN2019/1stlevel/${seed}gnc2084REST1Z_gm+tlrc \
s28 pain /data/tim/DPMN2019/1stlevel/${seed}gnc2084REST2Z_gm+tlrc \
s29 control /data/tim/DPMN2019/1stlevel/${seed}gnc2085REST1Z_gm+tlrc \
s29 pain /data/tim/DPMN2019/1stlevel/${seed}gnc2085REST2Z_gm+tlrc \
s30 control /data/tim/DPMN2019/1stlevel/${seed}gnc2087REST1Z_gm+tlrc \
s30 pain /data/tim/DPMN2019/1stlevel/${seed}gnc2087REST2Z_gm+tlrc \
s31 control /data/tim/DPMN2019/1stlevel/${seed}gnc2089REST1Z_gm+tlrc \
s31 pain /data/tim/DPMN2019/1stlevel/${seed}gnc2089REST2Z_gm+tlrc \
s32 control /data/tim/DPMN2019/1stlevel/${seed}gnc2093REST1Z_gm+tlrc \
s32 pain /data/tim/DPMN2019/1stlevel/${seed}gnc2093REST2Z_gm+tlrc \
s33 control /data/tim/DPMN2019/1stlevel/${seed}gnc3004REST1Z_gm+tlrc \
s33 pain /data/tim/DPMN2019/1stlevel/${seed}gnc3004REST2Z_gm+tlrc \
s34 control /data/tim/DPMN2019/1stlevel/${seed}gnc3006REST1Z_gm+tlrc \
s34 pain /data/tim/DPMN2019/1stlevel/${seed}gnc3006REST2Z_gm+tlrc \
s35 control /data/tim/DPMN2019/1stlevel/${seed}gnc3009REST1Z_gm+tlrc \
s35 pain /data/tim/DPMN2019/1stlevel/${seed}gnc3009REST2Z_gm+tlrc \
s36 control /data/tim/DPMN2019/1stlevel/${seed}gnc3010REST1Z_gm+tlrc \
s36 pain /data/tim/DPMN2019/1stlevel/${seed}gnc3010REST2Z_gm+tlrc \
s37 control /data/tim/DPMN2019/1stlevel/${seed}gnc3011REST1Z_gm+tlrc \
s37 pain /data/tim/DPMN2019/1stlevel/${seed}gnc3011REST2Z_gm+tlrc \
s38 control /data/tim/DPMN2019/1stlevel/${seed}gnc3014REST1Z_gm+tlrc \
s38 pain /data/tim/DPMN2019/1stlevel/${seed}gnc3014REST2Z_gm+tlrc \
s39 control /data/tim/DPMN2019/1stlevel/${seed}gnc3016REST1Z_gm+tlrc \
s39 pain /data/tim/DPMN2019/1stlevel/${seed}gnc3016REST2Z_gm+tlrc \
s40 control /data/tim/DPMN2019/1stlevel/${seed}gnc3017REST1Z_gm+tlrc \
s40 pain /data/tim/DPMN2019/1stlevel/${seed}gnc3017REST2Z_gm+tlrc \
s41 control /data/tim/DPMN2019/1stlevel/${seed}gnc3018REST1Z_gm+tlrc \
s41 pain /data/tim/DPMN2019/1stlevel/${seed}gnc3018REST2Z_gm+tlrc \
s42 control /data/tim/DPMN2019/1stlevel/${seed}gnc3019REST1Z_gm+tlrc \
s42 pain /data/tim/DPMN2019/1stlevel/${seed}gnc3019REST2Z_gm+tlrc \
s43 control /data/tim/DPMN2019/1stlevel/${seed}gnc3021REST1Z_gm+tlrc \
s43 pain /data/tim/DPMN2019/1stlevel/${seed}gnc3021REST2Z_gm+tlrc \
s44 control /data/tim/DPMN2019/1stlevel/${seed}gnc3023REST1Z_gm+tlrc \
s44 pain /data/tim/DPMN2019/1stlevel/${seed}gnc3023REST2Z_gm+tlrc \
s45 control /data/tim/DPMN2019/1stlevel/${seed}gnc3024REST1Z_gm+tlrc \
s45 pain /data/tim/DPMN2019/1stlevel/${seed}gnc3024REST2Z_gm+tlrc \
s46 control /data/tim/DPMN2019/1stlevel/${seed}gnc3025REST1Z_gm+tlrc \
s46 pain /data/tim/DPMN2019/1stlevel/${seed}gnc3025REST2Z_gm+tlrc \
s47 control /data/tim/DPMN2019/1stlevel/${seed}gnc3030REST1Z_gm+tlrc \
s47 pain /data/tim/DPMN2019/1stlevel/${seed}gnc3030REST2Z_gm+tlrc \
s48 control /data/tim/DPMN2019/1stlevel/${seed}gnc3031REST1Z_gm+tlrc \
s48 pain /data/tim/DPMN2019/1stlevel/${seed}gnc3031REST2Z_gm+tlrc \
s49 control /data/tim/DPMN2019/1stlevel/${seed}gnc3034REST1Z_gm+tlrc \
s49 pain /data/tim/DPMN2019/1stlevel/${seed}gnc3034REST2Z_gm+tlrc \
s50 control /data/tim/DPMN2019/1stlevel/${seed}gnc3035REST1Z_gm+tlrc \
s50 pain /data/tim/DPMN2019/1stlevel/${seed}gnc3035REST2Z_gm+tlrc \
done