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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
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I have 3dICC working. sorry for the false alarm.
Thanks.
by
pinghongyeh
-
AFNI Message Board
Dear AFNI users,
I have used the "file_tool" to fix the 3dICC run script but still got the errors
Error in if (len%%wd != 0) errex.AFNI(paste("The content under -dataTable is not rectangular !", :
argument is of length zero
Here is my script
3dICC -prefix ICC \
-jobs 6 \
-mask /Users/pyeh/bin/longDTI_npoint/mask.nii \
-model '1+age+(1|TimePoin
by
pinghongyeh
-
AFNI Message Board
Hi Gang,
It ran fine and output the results along with the FDR values. Sorry for the false alarm.
I have other questions regarding interpretating the contrasts. Here are the model and contrasts I used, there were 4 experimental groups and three time points, TP1, TP2, TP3
3dLMEr -prefix DTI_long \
-jobs 6 \
-mask /Users/pyeh/bin/longDTI_npoint/mask.nii \
-model 'Group*TimePoi
by
pinghongyeh
-
AFNI Message Board
Hi Gang,
I re-run the script but it seems that it still stuck at the step of "Loading required package: snow".
What syntax can I use to output the log?
Thank you.
Ping
by
pinghongyeh
-
AFNI Message Board
Hi Gang,
3dLMEr was stuck (hung) at the step of loading required package: snow for a day. I have already installed the package "snow", but I don't see R is cranking because no memory was chewing up at the background.
See attached for the script.
Here is the message:
Loading required package: lmerTest
Loading required package: lme4
Loading required package: Matr
by
pinghongyeh
-
AFNI Message Board
Any suggestions for fixing 3dMVM error? Thanks.
** Error:
Quitting due to model test failure...
Warning message:
NAs introduced by coercion
by
pinghongyeh
-
AFNI Message Board
Hi Gang,
Thanks for the reply.
3dMVM ran after changing "ID" to "Subj", however, it crashed early with the following error:
** Error:
Quitting due to model test failure...
Warning message:
NAs introduced by coercion
Thank you,
ping
by
pinghongyeh
-
AFNI Message Board
Dear AFNI users,
I have run into errors for running 3dMVM,
./3dMVM_runscript.sh
Loading required package: afex
Loading required package: lme4
Loading required package: Matrix
Loading required package: emmeans
************
Welcome to afex. For support visit:
- Functions for ANOVAs: aov_car(), aov_ez(), and aov_4()
- Methods for calculating p-values with mixed(): 'KR', &
by
pinghongyeh
-
AFNI Message Board
Dear AFNI users,
Parts of the pons and brainstem were chopped off after 3dSkullStrip (see the attached). Is there a way to be less stringent in skull stripping?
Thanks.
ping
by
pinghongyeh
-
AFNI Message Board
Hi Gang,
I have updated the ANFI, but the same errors still exist.
Thanks.
ping
by
pinghongyeh
-
AFNI Message Board
Hi Gang,
Version AFNI_2011_12_21_1014
[]
Here is the 3dMVM scripts I had, which was also attached in the previous email. Thanks.
3dMVM -prefix test -jobs 8 -model "group+gender+age" -qVars "age" -num_glt 1 -gltLabel 1 TBI_vs_HC -gltCode 1 'group : 1*TBI -1*HC' -dataTable \
subject group gender age InputFile \
subject_0004 TBI Male 45 /Data/HBOT/
by
pinghongyeh
-
AFNI Message Board
Hi,
I ran into errors while executing 3dMVM,
************
Loading required package: phia
Error in `$<-.data.frame`(`*tmp*`, "Subj", value = integer(0)) :
replacement has 0 rows, data has 95
Calls: $<- -> $<-.data.frame
Execution halted
I have attached the script I used.
Thanks a lot.
Ping
by
pinghongyeh
-
AFNI Message Board