3dLME for pre-post intervention design

AFNIbeginner · February 21, 2018, 8:24pm

Hello, I am new to AFNI and am trying to test whether pre- to post-treatment change in anxiety is correlated with change in seed-based resting state connectivity pre- to post-treatment. I set up the following model, but when I try to run it I get the following error “Incorrect level coding in variable session : T2”

Any help would be much appreciated!!

3dLME -prefix Anxiety1 -jobs 1
-model "SessionAnxiety"
-qVars “Anxiety”
-qVarCenters “31.40”
-ranEff ‘~1+Anxiety’
-SS_type 3
-num_glt 3
-gltLabel 1 ‘T1’ -gltCode 1 'Session : -1T1’
-gltLabel 2 ‘T2’ -gltCode 2 ‘Session : 1T2’
-gltLabel 3 ‘T1-Anxiety’ -gltCode 3 'Session : -1T1 Anxiety :’
-num_glf 1
-glfLabel 1 ‘Session_Anxiety’ -glfCode 1 ‘Session : -1T1 1T2 Anxiety :’
-dataTable
Subj Session Anxiety InputFile
04027 T1 45 /Applications/freesurfer/Study1/subs/04027_pre/aScript_results/PCC_seed.maskConnData.Z.nii.gz’[T1#0_Coef]’ \
04034 T1 31 /Applications/freesurfer/Study1/subs/04034_pre/aScript_results/PCC_seed.maskConnData.Z.nii.gz’[T1#0_Coef]’
04035 T1 40 /Applications/freesurfer/Study1/subs/04035_pre/aScript_results/PCC_seed.maskConnData.Z.nii.gz’[T1#0_Coef]’
04040 T1 28 /Applications/freesurfer/Study1/subs/04040_pre/aScript_results/PCC_seed.maskConnData.Z.nii.gz’[T1#0_Coef]’
04041 T1 18 /Applications/freesurfer/Study1/subs/04041_pre/aScript_results/PCC_seed.maskConnData.Z.nii.gz’[T1#0_Coef]’
04043 T1 26 /Applications/freesurfer/Study1/subs/04043_pre/aScript_results/PCC_seed.maskConnData.Z.nii.gz’[T1#0_Coef]’
04054 T1 32 /Applications/freesurfer/Study1/subs/04054_pre/aScript_results/PCC_seed.maskConnData.Z.nii.gz’[T1#0_Coef]’
04056 T1 23 /Applications/freesurfer/Study1/subs/04056_pre/aScript_results/PCC_seed.maskConnData.Z.nii.gz’[T1#0_Coef]’
04057 T1 41 /Applications/freesurfer/Study1/subs/04057_pre/aScript_results/PCC_seed.maskConnData.Z.nii.gz’[T1#0_Coef]’
04059 T1 29 /Applications/freesurfer/Study1/subs/04059_pre/aScript_results/PCC_seed.maskConnData.Z.nii.gz’[T1#0_Coef]’
04060 T1 32 /Applications/freesurfer/Study1/subs/04060_pre/aScript_results/PCC_seed.maskConnData.Z.nii.gz’[T1#0_Coef]’
04065 T1 32 /Applications/freesurfer/Study1/subs/04065_pre/aScript_results/PCC_seed.maskConnData.Z.nii.gz’[T1#0_Coef]’
04070 T1 30 /Applications/freesurfer/Study1/subs/04070_pre/aScript_results/PCC_seed.maskConnData.Z.nii.gz’[T1#0_Coef]’
04071 T1 28 /Applications/freesurfer/Study1/subs/04071_pre/aScript_results/PCC_seed.maskConnData.Z.nii.gz’[T1#0_Coef]’
04072 T1 38 /Applications/freesurfer/Study1/subs/04072_pre/aScript_results/PCC_seed.maskConnData.Z.nii.gz’[T1#0_Coef]’
04073 T1 31 /Applications/freesurfer/Study1/subs/04073_pre/aScript_results/PCC_seed.maskConnData.Z.nii.gz’[T1#0_Coef]’
04074 T1 29 /Applications/freesurfer/Study1/subs/04074_pre/aScript_results/PCC_seed.maskConnData.Z.nii.gz’[T1#0_Coef]’
04076 T1 42 /Applications/freesurfer/Study1/subs/04076_pre/aScript_results/PCC_seed.maskConnData.Z.nii.gz’[T1#0_Coef]’
04079 T1 30 /Applications/freesurfer/Study1/subs/04079_pre/aScript_results/PCC_seed.maskConnData.Z.nii.gz’[T1#0_Coef]’
04080 T1 27 /Applications/freesurfer/Study1/subs/04080_pre/aScript_results/PCC_seed.maskConnData.Z.nii.gz’[T1#0_Coef]’
04082 T1 28 /Applications/freesurfer/Study1/subs/04082_pre/aScript_results/PCC_seed.maskConnData.Z.nii.gz’[T1#0_Coef]’
04020 T2 18 /Applications/freesurfer/Study1/subs/04020_post/aScript_results/PCC_seed.maskConnData.Z.nii.gz’[T2#0_Coef]’
04027 T2 15 /Applications/freesurfer/Study1/subs/04027_post/aScript_results/PCC_seed.maskConnData.Z.nii.gz’[T2#0_Coef]’
04034 T2 33 /Applications/freesurfer/Study1/subs/04034_post/aScript_results/PCC_seed.maskConnData.Z.nii.gz’[T2#0_Coef]’
04035 T2 11 /Applications/freesurfer/Study1/subs/04035_post/aScript_results/PCC_seed.maskConnData.Z.nii.gz’[T2#0_Coef]’
04040 T2 20 /Applications/freesurfer/Study1/subs/04040_post/aScript_results/PCC_seed.maskConnData.Z.nii.gz’[T2#0_Coef]’
04041 T2 35 /Applications/freesurfer/Study1/subs/04041_post/aScript_results/PCC_seed.maskConnData.Z.nii.gz’[T2#0_Coef]’
04043 T2 28 /Applications/freesurfer/Study1/subs/04043_post/aScript_results/PCC_seed.maskConnData.Z.nii.gz’[T2#0_Coef]’
04054 T2 50 /Applications/freesurfer/Study1/subs/04054_post/aScript_results/PCC_seed.maskConnData.Z.nii.gz’[T2#0_Coef]’
04056 T2 25 /Applications/freesurfer/Study1/subs/04056_post/aScript_results/PCC_seed.maskConnData.Z.nii.gz’[T2#0_Coef]’
04057 T2 22 /Applications/freesurfer/Study1/subs/04057_post/aScript_results/PCC_seed.maskConnData.Z.nii.gz’[T2#0_Coef]’
04059 T2 23 /Applications/freesurfer/Study1/subs/04059_post/aScript_results/PCC_seed.maskConnData.Z.nii.gz’[T2#0_Coef]’
04060 T2 19 /Applications/freesurfer/Study1/subs/04060_post/aScript_results/PCC_seed.maskConnData.Z.nii.gz’[T2#0_Coef]’
04065 T2 19 /Applications/freesurfer/Study1/subs/04065_post/aScript_results/PCC_seed.maskConnData.Z.nii.gz’[T2#0_Coef]’
04070 T2 33 /Applications/freesurfer/Study1/subs/04070_post/aScript_results/PCC_seed.maskConnData.Z.nii.gz’[T2#0_Coef]’
04071 T2 11 /Applications/freesurfer/Study1/subs/04071_post/aScript_results/PCC_seed.maskConnData.Z.nii.gz’[T2#0_Coef]’
04072 T2 17 /Applications/freesurfer/Study1/subs/04072_post/aScript_results/PCC_seed.maskConnData.Z.nii.gz’[T2#0_Coef]’
04073 T2 21 /Applications/freesurfer/Study1/subs/04073_post/aScript_results/PCC_seed.maskConnData.Z.nii.gz’[T2#0_Coef]’
04074 T2 31 /Applications/freesurfer/Study1/subs/04074_post/aScript_results/PCC_seed.maskConnData.Z.nii.gz’[T2#0_Coef]’
04076 T2 39 /Applications/freesurfer/Study1/subs/04076_post/aScript_results/PCC_seed.maskConnData.Z.nii.gz’[T2#0_Coef]’
04079 T2 20 /Applications/freesurfer/Study1/subs/04079_post/aScript_results/PCC_seed.maskConnData.Z.nii.gz’[T2#0_Coef]’
04080 T2 24 /Applications/freesurfer/Study1/subs/04080_post/aScript_results/PCC_seed.maskConnData.Z.nii.gz’[T2#0_Coef]’
04082 T2 17 /Applications/freesurfer/Study1/subs/04082_post/aScript_results/PCC_seed.maskConnData.Z.nii.gz’[T2#0_Coef]’ \

Gang · February 21, 2018, 10:56pm

This test

-glfLabel 1 ‘Session_Anxiety’ -glfCode 1 ‘Session : -1T1 1T2 Anxiety :’ \

can be directly conducted as t-test:

-gltLabel 4 ‘Session_Anxiety’ -gltCode 4 ‘Session : -1T1 1T2 Anxiety :’ \

However, the error message is unrelated to the above testing setting. If the error persists, could you provide the output of the following command?

afni_system_check.py -check_all

AFNIbeginner · February 21, 2018, 11:52pm

Thank you very much for your help. When I run using a t-test I do get the same error message. Here is the output from running the system check:

-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 16.7.0
version: Darwin Kernel Version 16.7.0: Thu Jun 15 17:36:27 PDT 2017; root:xnu-3789.70.16~2/RELEASE_X86_64
distribution: 10.12.6 x86_64
number of CPUs: 8
apparent login shell: tcsh
shell RC file: .cshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /Users/User1/abin/afni
afni version : Precompiled binary macosx_10.7_local: Nov 21 2017
: AFNI_17.3.04
AFNI_version.txt : AFNI_17.3.04, macosx_10.7_local, Nov 21 2017
which python : /usr/bin/python
python version : 2.7.10
which R : /usr/local/bin/R
R version : R version 3.4.1 (2017-06-30) – “Single Candle”
which tcsh : /bin/tcsh

instances of various programs found in PATH:
afni : 1 (/Users/User1/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.4/Resources/bin/R)
python : 1 (/usr/bin/python)
python2 : 0
python3 : 0

testing ability to start various programs…
afni : success
suma : success
3dSkullStrip : success
uber_subject.py : success
3dAllineate : success
3dRSFC : success
SurfMesh : success
3dClustSim : success

checking for R packages…
rPkgsInstall -pkgs ALL -check : success

checking for $HOME files…
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found

------------------------------ python libs -------------------------------
** python module not found: PyQt4
– PyQt4 is no longer needed for an AFNI bootcamp

python binaries under /sw/bin:
/sw/bin/python (sym link to /sw/bin/python2.7)

-------------------------------- env vars --------------------------------
PATH = /usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/User1/abin

PYTHONPATH = /sw/lib/qt4-mac/lib/python2.7/site-packages

R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH (sub-shell) = /opt/X11/lib/flat_namespace
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) =

------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME
top history: … [rickr]: updated FT_white.nii w/out 16 (brain stem)
data dir : found AFNI_demos under $HOME
top history: … [pault]: remove rank from FATCAT_DEMO, FAT_MVM_DEMO
data dir : found suma_demo under $HOME
top history: …/SUMA_data/Build_tmp on Wed Aug 20 10:04:23 EDT 2014
data dir : found afni_handouts under $HOME
atlas : found TT_N27+tlrc under /Users/User1/abin

------------------------------ OS specific -------------------------------

++ found 1 dylib files under ‘/opt/X11/lib/flat_namespace’
– found ‘libXt’ dylib files:
/opt/X11/lib/flat_namespace/libXt.6.dylib
– recent OS X, cheating to check DYLD_LIBRARY_PATH in cur shell ‘tcsh’…
++ found evar DYLD_LIBRARY_PATH = /opt/X11/lib/flat_namespace

========================= summary, please fix: =========================

consider installing fink

Gang · February 22, 2018, 4:51pm

I’m puzzled because your 3dLME script works fine on my computer. Are you sure that the information you pasted about “afni_system_check.py -check_all” came from the same computer you ran 3dLME on?

AFNIbeginner · February 22, 2018, 8:21pm

Thank you again for your help, I very much appreciate it.

The information was both from the same computer. Could it be an issue with the layout of my data table? I tried including the table as a separate file now and am getting the following error (I have also copied the data table below the error message):

…
-gltCode 4 Session : -1T1 1T2 Anxiety : -dataTable @datatable.txt
Read 263 items
Error in if (len%%wd != 0) errex.AFNI(paste(“The content under -dataTable is not rectangular !”, :
argument is of length zero
Calls: process.LME.opts
In addition: Warning messages:
1: In scan(ff, what = “character”, na.strings = “”) :
EOF within quoted string
2: In scan(ff, what = “character”, na.strings = “”) :
embedded nul(s) found in input
3: In grep(“[^\\]”, opts) : input string 1 is invalid in this locale
Execution halted

Here is the data table:

Subj Session Anxiety InputFile
4027 T1 16 /Applications/freesurfer/ERT/subs/04027_pre/MattsScript_results/PCC_seed.maskConnData.Z.nii.gz
4034 T1 19 /Applications/freesurfer/ERT/subs/04034_pre/MattsScript_results/PCC_seed.maskConnData.Z.nii.gz
4035 T1 23 /Applications/freesurfer/ERT/subs/04035_pre/MattsScript_results/PCC_seed.maskConnData.Z.nii.gz
4040 T1 28 /Applications/freesurfer/ERT/subs/04040_pre/MattsScript_results/PCC_seed.maskConnData.Z.nii.gz
4041 T1 18 /Applications/freesurfer/ERT/subs/04041_pre/MattsScript_results/PCC_seed.maskConnData.Z.nii.gz
4043 T1 11 /Applications/freesurfer/ERT/subs/04043_pre/MattsScript_results/PCC_seed.maskConnData.Z.nii.gz
4054 T1 17 /Applications/freesurfer/ERT/subs/04054_pre/MattsScript_results/PCC_seed.maskConnData.Z.nii.gz
4056 T1 23 /Applications/freesurfer/ERT/subs/04056_pre/MattsScript_results/PCC_seed.maskConnData.Z.nii.gz
4057 T1 19 /Applications/freesurfer/ERT/subs/04057_pre/MattsScript_results/PCC_seed.maskConnData.Z.nii.gz
4059 T1 28 /Applications/freesurfer/ERT/subs/04059_pre/MattsScript_results/PCC_seed.maskConnData.Z.nii.gz
4060 T1 25 /Applications/freesurfer/ERT/subs/04060_pre/MattsScript_results/PCC_seed.maskConnData.Z.nii.gz
4065 T1 32 /Applications/freesurfer/ERT/subs/04065_pre/MattsScript_results/PCC_seed.maskConnData.Z.nii.gz
4070 T1 30 /Applications/freesurfer/ERT/subs/04070_pre/MattsScript_results/PCC_seed.maskConnData.Z.nii.gz
4071 T1 26 /Applications/freesurfer/ERT/subs/04071_pre/MattsScript_results/PCC_seed.maskConnData.Z.nii.gz
4072 T1 33 /Applications/freesurfer/ERT/subs/04072_pre/MattsScript_results/PCC_seed.maskConnData.Z.nii.gz
4073 T1 30 /Applications/freesurfer/ERT/subs/04073_pre/MattsScript_results/PCC_seed.maskConnData.Z.nii.gz
4074 T1 25 /Applications/freesurfer/ERT/subs/04074_pre/MattsScript_results/PCC_seed.maskConnData.Z.nii.gz
4076 T1 20 /Applications/freesurfer/ERT/subs/04076_pre/MattsScript_results/PCC_seed.maskConnData.Z.nii.gz
4079 T1 30 /Applications/freesurfer/ERT/subs/04079_pre/MattsScript_results/PCC_seed.maskConnData.Z.nii.gz
4080 T1 25 /Applications/freesurfer/ERT/subs/04080_pre/MattsScript_results/PCC_seed.maskConnData.Z.nii.gz
4082 T1 28 /Applications/freesurfer/ERT/subs/04082_pre/MattsScript_results/PCC_seed.maskConnData.Z.nii.gz
4020 T2 45 /Applications/freesurfer/ERT/subs/04020_post/MattsScript_results/PCC_seed.maskConnData.Z.nii.gz
4027 T2 35 /Applications/freesurfer/ERT/subs/04027_post/MattsScript_results/PCC_seed.maskConnData.Z.nii.gz
4034 T2 53 /Applications/freesurfer/ERT/subs/04034_post/MattsScript_results/PCC_seed.maskConnData.Z.nii.gz
4035 T2 42 /Applications/freesurfer/ERT/subs/04035_post/MattsScript_results/PCC_seed.maskConnData.Z.nii.gz
4040 T2 27 /Applications/freesurfer/ERT/subs/04040_post/MattsScript_results/PCC_seed.maskConnData.Z.nii.gz
4041 T2 45 /Applications/freesurfer/ERT/subs/04041_post/MattsScript_results/PCC_seed.maskConnData.Z.nii.gz
4043 T2 33 /Applications/freesurfer/ERT/subs/04043_post/MattsScript_results/PCC_seed.maskConnData.Z.nii.gz
4054 T2 54 /Applications/freesurfer/ERT/subs/04054_post/MattsScript_results/PCC_seed.maskConnData.Z.nii.gz
4056 T2 33 /Applications/freesurfer/ERT/subs/04056_post/MattsScript_results/PCC_seed.maskConnData.Z.nii.gz
4057 T2 18 /Applications/freesurfer/ERT/subs/04057_post/MattsScript_results/PCC_seed.maskConnData.Z.nii.gz
4059 T2 46 /Applications/freesurfer/ERT/subs/04059_post/MattsScript_results/PCC_seed.maskConnData.Z.nii.gz
4060 T2 31 /Applications/freesurfer/ERT/subs/04060_post/MattsScript_results/PCC_seed.maskConnData.Z.nii.gz
4065 T2 49 /Applications/freesurfer/ERT/subs/04065_post/MattsScript_results/PCC_seed.maskConnData.Z.nii.gz
4070 T2 44 /Applications/freesurfer/ERT/subs/04070_post/MattsScript_results/PCC_seed.maskConnData.Z.nii.gz
4071 T2 33 /Applications/freesurfer/ERT/subs/04071_post/MattsScript_results/PCC_seed.maskConnData.Z.nii.gz
4072 T2 34 /Applications/freesurfer/ERT/subs/04072_post/MattsScript_results/PCC_seed.maskConnData.Z.nii.gz
4073 T2 42 /Applications/freesurfer/ERT/subs/04073_post/MattsScript_results/PCC_seed.maskConnData.Z.nii.gz
4074 T2 35 /Applications/freesurfer/ERT/subs/04074_post/MattsScript_results/PCC_seed.maskConnData.Z.nii.gz
4076 T2 39 /Applications/freesurfer/ERT/subs/04076_post/MattsScript_results/PCC_seed.maskConnData.Z.nii.gz
4079 T2 28 /Applications/freesurfer/ERT/subs/04079_post/MattsScript_results/PCC_seed.maskConnData.Z.nii.gz
4080 T2 47 /Applications/freesurfer/ERT/subs/04080_post/MattsScript_results/PCC_seed.maskConnData.Z.nii.gz
4082 T2 31 /Applications/freesurfer/ERT/subs/04082_post/MattsScript_results/PCC_seed.maskConnData.Z.nii.gz

Gang · February 22, 2018, 8:50pm

For this new error with data table saved as a separate file, you need to add a backslash, at the end of the last line. However, for the original error, it has something to do with one of the following two lines:

-gltLabel 2 ‘T2’ -gltCode 2 ‘Session : 1T2’
…
-gltLabel 4 ‘Session_Anxiety’ -gltCode 4 'Session : -1T1 1*T2 Anxiety :’ \

AFNIbeginner · February 27, 2018, 8:07pm

Thank you very much! It seems to be working now. And I apologize for my delayed response.

I have one more follow-up question-- if I now want to extract beta values from an ROI and use FWE correction, what would be the best way to do this?

Thank you again,
AFNIbeginner

Gang · February 28, 2018, 8:32pm

if I now want to extract beta values from an ROI and use FWE correction, what would be the best way to do this?

Those two things don’t mix well to me. For FWE correction, why do you need to extract the values for an ROI?

AFNIbeginner · March 1, 2018, 8:48pm

Oh, I meant them separately. To first do an FWE correction for voxels within an ROI and then to extract the betas for visualization purposes. Does it make sense to do it that way?

Gang · March 2, 2018, 2:07pm

To first do an FWE correction for voxels within an ROI and then to extract the betas for
visualization purposes. Does it make sense to do it that way?

Sure, that’s legitimate. You can use, for example, 3dROIstats, to extract the effect estimates for that purpose.

AFNIbeginner · March 5, 2018, 6:24pm

Thank you very much!

AFNIbeginner · March 7, 2018, 7:16pm

Hello again. I think the analyses worked, but I am just hoping to double-check that the model is doing what I think it is doing (copied again below). Since I have anxiety at time one (T1) and time two (T2) for each subject, is this model testing change in anxiety T2-T1 or is it T2/T1 or something else? We are hoping to test whether increases in functional connectivity are associated with decreases in anxiety over time.

Thank you again.

-gltLabel 4 ‘Session_Anxiety’ -gltCode 4 ‘Session : -1T1 1T2 Anxiety :’ \
-dataTable \
Subj Session Anxiety InputFile \
04027 T1 45 /Applications/freesurfer/Study1/subs/04027_pre/aScript_results/PCC_seed.maskConnData.Z.nii.gz \
04034 T1 31 /Applications/freesurfer/Study1/subs/04034_pre/aScript_results/PCC_seed.maskConnData.Z.nii.gz \
04035 T1 40 /Applications/freesurfer/Study1/subs/04035_pre/aScript_results/PCC_seed.maskConnData.Z.nii.gz \
…
04020 T2 18 /Applications/freesurfer/Study1/subs/04020_post/aScript_results/PCC_seed.maskConnData.Z.nii.gz’ \
04027 T2 15 /Applications/freesurfer/Study1/subs/04027_post/aScript_results/PCC_seed.maskConnData.Z.nii.gz’ \
04034 T2 33 /Applications/freesurfer/Study1/subs/04034_post/aScript_results/PCC_seed.maskConnData.Z.nii.gz’ \
04035 T211 /Applications/freesurfer/Study1/subs/04035_post/aScript_results/PCC_seed.maskConnData.Z.nii.gz’
…

Gang · March 8, 2018, 6:18pm

-gltLabel 4 ‘Session_Anxiety’ -gltCode 4 ‘Session : -1T1 1T2 Anxiety :’ \

It tests whether the two time points have the same Anxiety effect (slope).

AFNIbeginner · March 13, 2018, 12:05am

I see. So if I wanted to test change in anxiety (AnxietyPost-AnxietyPre). Would it make sense to add an extra anxiety column and dummy-code, like this?

Thank you again and sorry for the basic questions.

-gltLabel 4 ‘Session_Anxiety’ -gltCode 4 ‘Session : -1T1 1T2 -1AnxietyPre 1AnxietyPost :’ \
-dataTable \
Subj Session AnxietyPre AnxietyPost InputFile \
04027 T1 45 0 /Applications/freesurfer/Study1/subs/04027_pre/aScript_results/PCC_seed.maskConnData.Z.nii.gz \
04034 T1 31 0 /Applications/freesurfer/Study1/subs/04034_pre/aScript_results/PCC_seed.maskConnData.Z.nii.gz \
04035 T1 40 0 /Applications/freesurfer/Study1/subs/04035_pre/aScript_results/PCC_seed.maskConnData.Z.nii.gz \
…
04020 T2 0 18 /Applications/freesurfer/Study1/subs/04020_post/aScript_results/PCC_seed.maskConnData.Z.nii.gz’ \
04027 T2 0 15 /Applications/freesurfer/Study1/subs/04027_post/aScript_results/PCC_seed.maskConnData.Z.nii.gz’ \
04034 T2 0 33 /Applications/freesurfer/Study1/subs/04034_post/aScript_results/PCC_seed.maskConnData.Z.nii.gz’ \
04035 T2 0 11 /Applications/freesurfer/Study1/subs/04035_post/aScript_results/PCC_seed.maskConnData.Z.nii.gz’ \
…

Gang · March 13, 2018, 9:39pm

if I wanted to test change in anxiety (AnxietyPost-AnxietyPre). Would it make sense to add
an extra anxiety column and dummy-code, like this?

What do you mean by “Pre” and “Post”? Are they the two time points? If so, the original test

-gltLabel 4 ‘Session_Anxiety’ -gltCode 4 ‘Session : -1T1 1T2 Anxiety :’ \

is what you want unless you mean something else.

AFNIbeginner · March 14, 2018, 4:08pm

They are two time points (one before an intervention and one 8-weeks later, after the intervention).

Sounds good, I just wanted to be sure-- I’ll go with the original then. Thank you very much!

AFNIbeginner · April 6, 2018, 4:18pm

Hello,

I am now trying to interpret the output from these analyses and am not sure whether to look at:

#1 (Intercept) F
#3 Session: Anxiety F
#8 T1-Anxiety
#9 T1-Anxiety Z
#10 Session_Anxiety
#11 Session_Anxiety Z

Our primary question is how connectivity from T1 to T2 is associated with change in anxiety from T1 to T2.

Also, I had entered the mean value for qVarCenters, but since there are important differences between the mean of Anxiety at T1 and T2, should I be entering two separate means here? Or not have the qVarCenters option?

Lastly, in regards to thresholding, what would you recommend as a threshold?

Thank you very much again for your help.

Gang · April 6, 2018, 8:17pm

I am now trying to interpret the output from these analyses and am not sure whether to look at:

#1 (Intercept) F

This is the intercept in the model, which is of no interest to most people.

#3 Session: Anxiety F

Interaction between Session and Anxiety

#8 T1-Anxiety
#9 T1-Anxiety Z
#10 Session_Anxiety
#11 Session_Anxiety Z

You specified these tests through -gltCode, so you should know what you meant to get.

Our primary question is how connectivity from T1 to T2 is associated with change in anxiety from T1 to T2.

Is the following what you want:

-gltLabel 4 ‘Session_Anxiety’ -gltCode 4 ‘Session : -1T1 1T2 Anxiety :’ \

I had entered the mean value for qVarCenters, but since there are important differences between the
mean of Anxiety at T1 and T2, should I be entering two separate means here? Or not have the qVarCenters option?

I recommend that you center Anxiety at T1 and T2 separately, and then feed the numbers into the table for 3dLME.

in regards to thresholding, what would you recommend as a threshold?

Personally I don’t like thresholding because of its arbitrariness. For publication purpose, you can use p-value of 0.01 or below.

AFNIbeginner · April 6, 2018, 10:30pm

Thank you, so gltLabel4 corresponds to “#10 Session_Anxiety”?

And since both Anxiety at T1 and T2 are under the heading of “Anxiety”, how do I enter the mean anxiety for T1 and T2 separately in 3dLME?

I appreciate your help.

Gang · April 9, 2018, 1:36pm

so gltLabel4 corresponds to “#10 Session_Anxiety”?

Since you created this label “Session_Anxiety” in one of those glt specifications, only you can answer this question.

since both Anxiety at T1 and T2 are under the heading of “Anxiety”, how do I enter the mean anxiety for T1 and T2 separately in 3dLME?

Remove the center (e.g., mean) of “Anxiety” for T1 and T2 separately outside of 3dLME using whatever program you like (e.g., R, Python, Excel, Matlab), and then feed those numbers back into the table in 3dLME.