AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

History of AFNI updates  

|
May 21, 2018 02:18PM
We are trying to run 3dLME but are stopped by a model test error. We suspect "Inappropriate model specification" but do not see why.
Any insights or obvious issues?

Thanks!

3dLME -overwrite -prefix ../ncanda_scripts/ncanda_3dlme_output/3dlme_output_extxagexcor_continuous.nii.gz \
      -mask gm_50mask+tlrc \
      -model 'Ext_t*ageatvisit*correct+reward+meanmotion' \
      -qVars "Ext_t,ageatvisit,meanmotion" \
      -ranEff '~1' \
      -jobs 8 \
      -SS_type 3 \
      -dataTable @datatable_3dlme_resp2018419.txt

where dataTable looks like

Subj   ageat… visit Ext_t Int_t Risk_… Ext_… Int_… meanm… corr… rewa… InputF…
  <fctr>  <dbl> <int> <dbl> <dbl> <fctr> <fct> <fct>  <dbl> <fct> <fct> <fctr>
1 A002    0.110     2  3.87  3.93 no     no    no    0.182  corr… neut… ../A00…
2 A002    0.110     2  3.87  3.93 no     no    no    0.182  corr… rewa… ../A00…
3 A002    0.110     2  3.87  3.93 no     no    no    0.182  erro… neut… ../A00…
4 A002    0.110     2  3.87  3.93 no     no    no    0.182  erro… rewa… ../A00…
5 A004    0.404     2  3.89  3.71 yes    no    no    0.0938 corr… neut… ../A00…
6 A004    0.404     2  3.89  3.71 yes    no    no    0.0938 corr… rewa… ../A00…


Ultimately we have 194 InputFiles repeated 4 times for each cat. vars reward and correct
read.table("datatable_3dlme_resp2018419.txt",header=T) %>% group_by(reward,correct) %>% summarise(n=length(InputFile)) %>% filter(n!=1)
  reward  correct           n
  <fctr>  <fctr>        <int>
1 neutral correct         194
2 neutral error_correct   194
3 reward  correct         194
4 reward  error_correct   194

3dLME's model test fails:

***** End of data structure information *****
++++++++++++++++++++++++++++++++++++++++++++++++++++

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 nlme and phia have been installed. See the 3dLME
help documentation for more details.

1) Inappropriate model specification with options -model, or -qVars.

2) In correct 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 hader
would cause grief for 3dLME.

** Error:
   Quitting due to model test failure...
Subject Author Posted

3dlme model test fail

alq6 May 21, 2018 02:18PM

Re: 3dlme model test fail

gang May 21, 2018 04:21PM

Re: 3dlme model test fail

alq6 May 23, 2018 09:59AM

Re: 3dlme model test fail

gang May 23, 2018 03:35PM

Re: 3dlme model test fail

alq6 May 29, 2018 02:41PM

Re: 3dlme model test fail

gang May 30, 2018 05:30PM