Hello!
I'm encountering some issues with running 3dMVM where it will read the input files but throw the following error:
Reading input files now...
Reading input files: Done!
If the program hangs here for more than, for example, half an hour,
kill the process because the model specification or the GLT coding
is likely inappropriate.
~~~~~~~~~~~~~~~~~~~ Model test failed! ~~~~~~~~~~~~~~~~~~~
Possible reasons:
0) Make sure that R packages afex and phia have been installed. See the 3dMVM
help documentation for more details.
1) Inappropriate model specification with options -bsVars, -wsVars, or -qVars.
Note that within-subject or repeated-measures variables have to be declared
with -wsVars.
2) Incorrect specifications in general linear test coding with -gltCode.
3) Mistakes in data table. Check the data structure shown above, and verify
whether there are any inconsistencies.
4) Inconsistent variable names which are case sensitive. For example, factor
named Group in model specification and then listed as group in the table header
would cause grief for 3dMVM.
5) Not enough number of subjects. This may happen when there are two or more
withi-subject factors. For example, a model with two within-subject factors with
m and n levels respectively requires more than (m-1)*(n-1) subjects to be able to
model the two-way interaction with the multivariate approach.
I believe that each of the possible reasons for model test failure are satisfied, so I'm confused as to what could be causing the issue. Any ideas for what might be the cause?
For reference, this is what my code looks like:
3dMVM -prefix PREFIXNAME -jobs 5 \
-bsVars "Group+Sex+MEdu" \
-num_glt 2 \
-gltLabel 1 HR -gltCode 1 'Group : 1*HR' \
-gltLabel 2 LR -gltCode 2 'Group : 1*LR' \
-dataTable @datatable.txt
where datatable.txt is:
Subj Group Sex MEdu InputFile
sub01 LR Male 2 sub01/ROI.nii.gz
sub02 HR Male 4 sub02/ROI.nii.gz
sub03 LR Male 4 sub03/ROI.nii.gz
sub04 HR Male 4 sub04/ROI.nii.gz
sub05 HR Male 3 sub05/ROI.nii.gz
sub06 LR Male 3 sub06/ROI.nii.gz
sub07 HR Male 3 sub07/ROI.nii.gz
sub08 HR Male 4 sub08/ROI.nii.gz
sub09 HR Male 4 sub09/ROI.nii.gz
sub10 HR Female 3 sub10/ROI.nii.gz
sub11 HR Male 4 sub11/ROI.nii.gz
sub12 HR Male 3 sub12/ROI.nii.gz
sub13 HR Male 4 sub13/ROI.nii.gz
sub14 HR Female 2 sub14/ROI.nii.gz
sub15 HR Male 2 sub15/ROI.nii.gz
sub16 LR Female 4 sub16/ROI.nii.gz
sub17 HR Male 2 sub17/ROI.nii.gz
sub18 LR Female 4 sub18/ROI.nii.gz
sub19 HR Male 4 sub19/ROI.nii.gz
sub20 LR Female 4 sub20/ROI.nii.gz
sub21 HR Female 4 sub21/ROI.nii.gz
sub22 HR Male 3 sub22/ROI.nii.gz
sub23 HR Female 2 sub23/ROI.nii.gz
sub24 HR Female 3 sub24/ROI.nii.gz
sub25 HR Male 3 sub25/ROI.nii.gz
sub26 HR Male 4 sub26/ROI.nii.gz
sub27 HR Male 2 sub27/ROI.nii.gz
sub28 HR Female 2 sub28/ROI.nii.gz
sub29 HR Female 3 sub29/ROI.nii.gz
sub30 HR Female 3 sub30/ROI.nii.gz
sub31 HR Male 2 sub31/ROI.nii.gz
sub32 HR Female 3 sub32/ROI.nii.gz
sub33 HR Male 2 sub33/ROI.nii.gz
sub34 HR Male 3 sub34/ROI.nii.gz
sub35 HR Female 3 sub35/ROI.nii.gz
sub36 LR Female 3 sub36/ROI.nii.gz
sub37 HR Male 3 sub37/ROI.nii.gz
sub38 HR Male 4 sub38/ROI.nii.gz
sub39 HR Male 2 sub39/ROI.nii.gz
sub40 HR Male 3 sub40/ROI.nii.gz
sub41 LR Male 4 sub41/ROI.nii.gz
sub42 LR Male 4 sub42/ROI.nii.gz
sub43 LR Male 2 sub43/ROI.nii.gz
sub44 HR Female 4 sub44/ROI.nii.gz
sub45 HR Female 4 sub45/ROI.nii.gz
sub46 HR Female 2 sub46/ROI.nii.gz
sub47 HR Female 3 sub47/ROI.nii.gz
sub48 HR Female 2 sub48/ROI.nii.gz
sub49 HR Male 3 sub49/ROI.nii.gz
sub50 HR Female 2 sub50/ROI.nii.gz
sub51 HR Male 3 sub51/ROI.nii.gz
sub52 HR Male 2 sub52/ROI.nii.gz
sub53 HR Male 2 sub53/ROI.nii.gz
sub54 HR Male 3 sub54/ROI.nii.gz
sub55 HR Male 3 sub55/ROI.nii.gz
sub56 HR Male 2 sub56/ROI.nii.gz
sub57 HR Male 2 sub57/ROI.nii.gz
sub58 LR Female 4 sub58/ROI.nii.gz
sub59 LR Female 3 sub59/ROI.nii.gz
sub60 LR Male 2 sub60/ROI.nii.gz
sub61 LR Male 3 sub61/ROI.nii.gz
sub62 LR Male 3 sub62/ROI.nii.gz
sub63 HR Male 4 sub63/ROI.nii.gz
sub64 HR Male 4 sub64/ROI.nii.gz
sub65 HR Male 4 sub65/ROI.nii.gz
sub66 HR Male 4 sub66/ROI.nii.gz
sub67 HR Male 3 sub67/ROI.nii.gz
sub68 LR Male 4 sub68/ROI.nii.gz
sub69 HR Male 2 sub69/ROI.nii.gz
sub70 HR Female 3 sub70/ROI.nii.gz
sub71 LR Female 4 sub71/ROI.nii.gz
sub72 LR Female 4 sub72/ROI.nii.gz
sub73 HR Female 3 sub73/ROI.nii.gz
sub74 HR Male 4 sub74/ROI.nii.gz
sub75 LR Male 3 sub75/ROI.nii.gz
sub76 LR Female 3 sub76/ROI.nii.gz
sub77 LR Male 3 sub77/ROI.nii.gz
sub78 HR Female 4 sub78/ROI.nii.gz
sub79 LR Male 3 sub79/ROI.nii.gz
sub80 LR Male 3 sub80/ROI.nii.gz
sub81 LR Male 4 sub81/ROI.nii.gz
sub82 HR Male 3 sub82/ROI.nii.gz
sub83 HR Female 4 sub83/ROI.nii.gz
sub84 HR Male 2 sub84/ROI.nii.gz
sub85 HR Female 2 sub85/ROI.nii.gz
sub86 LR Male 4 sub86/ROI.nii.gz
sub87 LR Male 3 sub87/ROI.nii.gz
I also ran afni_system_check.py -check_all to see whether there might be an issue with my version of R (since I had run into that issue in the past), and here is the output of that (and everything seems to look ok?):
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 19.6.0
version: Darwin Kernel Version 19.6.0: Thu May 6 00:48:39 PDT 2021; root:xnu-6153.141.33~1/RELEASE_X86_64
distribution: 10.15.7 x86_64
number of CPUs: 16
apparent login shell: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /Users/liuj10/abin/afni
afni version : Precompiled binary macosx_10.7_local: Aug 28 2018
: AFNI_18.2.15
AFNI_version.txt : AFNI_18.2.15, macosx_10.7_local, Aug 28 2018
which python : /usr/bin/python
python version : 2.7.16
which R : /usr/local/bin/R
R version : R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
which tcsh : /bin/tcsh
instances of various programs found in PATH:
afni : 1 (/Users/liuj10/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.6/Resources/bin/R)
python : 1 (/System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
python2 : 1 (/System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
python3 : 2
/usr/local/Cellar/python@3.9/3.9.5/Frameworks/Python.framework/Versions/3.9/bin/python3.9
/usr/bin/python3
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
-------------------------------- env vars --------------------------------
PATH = /usr/local/ANTs/bin:/Users/liuj10/opt/anaconda2/condabin:/usr/local/fsl/bin:/usr/local/DTIPrepTools-0.1.1-Linux/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Applications/MATLAB_R2019a.app/bin:/opt/X11/bin:/Users/liuj10/abin:/Users/liuj10/abin
PYTHONPATH =
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 : missing AFNI_data6
data dir : missing AFNI_demos
data dir : missing suma_demo
data dir : missing afni_handouts
atlas : found TT_N27+tlrc under /Users/liuj10/abin
------------------------------ OS specific -------------------------------
which brew : /usr/local/bin/brew
brew version : Homebrew 3.1.12
-- for PyQt4 under brew, consider running:
brew install cartr/qt4/pyqt
-- consider installing gcc under homebrew
++ found valid link /usr/local/lib/libglib-2.0.dylib
to ../Cellar/glib/2.68.3/lib/libglib-2.0.dylib
++ 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 'bash'...
++ found evar DYLD_LIBRARY_PATH = /opt/X11/lib/flat_namespace
-- recent OS X, cheating to check DYLD_LIBRARY_PATH in shell 'tcsh'...
++ found evar DYLD_LIBRARY_PATH = /opt/X11/lib/flat_namespace
========================= summary, please fix: =========================
* login shell 'bash', trusting user to translate from 'tcsh'
* shell bash: consider sourcing (non-login) .bashrc from (login) .bash_profile
* insufficient data for AFNI bootcamp
Any ideas as to what could be incorrect in my 3dMVM code or why I'm getting this error?
Thank you!
Janelle
