ClusterExplorer Zscr problem

AFNI Message Board
1

Hi,
Just redirecting a thread to a new one.

Original question was:

Dear Justin,
this morning we run Cluster Explorer with the results derived from one sample t-test executed with 3dttest++. It didn’t work, likely because the output was Zscr. We have tried to run it with an output based on t stat, but we obtained the following error message when executing @ClustExp_run_shiny:

Attaching package: ‘afex’
The following object is masked from ‘package:lme4’:
lmer
Error in factor(mean.df$Group, levels = c(lab.a, lab.b), ordered = TRUE) :
objeto ‘lab.a’ no encontrado
Calls: … sourceUTF8 → eval → eval → …stacktraceon… → factor
Ejecución interrumpida

Could you indicate me the potential source of my error?
Thanks a lot in advance.
Karel

2

Hi,
Both the Zscr and the one sample ttest problems are on my end…

It never occurred to me to look at a one sample test with box plots, but it makes total sense.
I may have left it out because I haven’t yet added support for covariate files.
The error caused by the program looking for 2 labels for the 2 groups in the case of 3dttest++

I can try to get fixes in over the weekend.
The Zscr fix should be easy.
The one sample fix may take a little testing, as it may break other shiny things.

Thanks, Justin

3

Hi Justin,

Thank you so much for your reply. I have tried to use the cluster explorer with two sample or paired ttest and it worked. The future fix for the Zscores and One sample ttest would be great and useful for us.

Thanks a lot,
Karel

4

Hi Justin,

As I replied before, this time the I did not have error when I ran the script. But, for some reason the web page does not create plots. Maybe I am doing something wrong. I would like to ask, In which space should the Tstat map must be? MNI, Talairach, original? I realized that these messages appeared in the end of the script execution.


PO: plugout connection from host 127.0.0.1 (tcp:*:7955)
PO: plugout connection name is plugout_drive
*+ WARNING: Forced switch from 'Original View' to 'Talairach View' [#1]
*+ WARNING: Forced switch from 'Talairach View' to 'Original View' [#2]
PO: plugout 'plugout_drive' has broken connection!
  : iochan_goodcheck: no longer alive

Listening on http://127.0.0.1:5519
reactivePrint is deprecated. Please use renderPrint instead. To disable this message, run options(shiny.deprecation.messages=FALSE)
PO: plugout connection from host 127.0.0.1 (tcp:*:7955)
PO: plugout connection name is plugout_drive
*+ WARNING: Bad drive AFNI result from 'SET_SPM_XYZ A.'
PO: plugout 'plugout_drive' has broken connection!
  : iochan_goodcheck: no longer alive
No trace type specified:
  Based on info supplied, a 'scatter' trace seems appropriate.
  Read more about this trace type -> https://plot.ly/r/reference/#scatter
No scatter mode specifed:
  Setting the mode to markers
  Read more about this attribute -> https://plot.ly/r/reference/#scatter-mode
PO: plugout connection from host 127.0.0.1 (tcp:*:7955)
PO: plugout connection name is plugout_drive
PO: plugout 'plugout_drive' has broken connection!
  : iochan_goodcheck: no longer alive
No trace type specified:
  Based on info supplied, a 'scatter' trace seems appropriate.
  Read more about this trace type -> https://plot.ly/r/reference/#scatter
No scatter mode specifed:
  Setting the mode to markers
  Read more about this attribute -> https://plot.ly/r/reference/#scatter-mode

Do you know what could be the error?

Thanks a lot,
Karel