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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:

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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

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Alfonso Alfini
March 06, 2016 06:21AM
Hello Afni Experts,

I used proc.py to generate a stats+tlrc image from a task based experiment. I am trying to use 3dLME for my group analysis, however when I execute the script I get the following feedback:

255a-280:3dLME_2.13.16 EGI$ ./step2.group_LME.sh
Loading required package: nlme
Package nlme loaded successfully!

Loading required package: phia
Loading required package: car
Package phia loaded successfully!

Warning message:
package ‘car’ was built under R version 3.1.3

++++++++++++++++++++++++++++++++++++++++++++++++++++
***** Summary information of data structure *****
14 subjects : S003 S004 S005 S006 S007 S008 S009 S010 S011 S012 S013 S014 S015 S016
56 response values
2 levels for factor Time : Post Pre
2 levels for factor Level : H L
4 post hoc tests

Contingency tables of subject distributions among the categorical variables:


Tabulation of subjects against all categorical variables
~~~~~~~~~~~~~~
Subj vs Time:

Post Pre
S003 2 2
S004 2 2
S005 2 2
S006 2 2
S007 2 2
S008 2 2
S009 2 2
S010 2 2
S011 2 2
S012 2 2
S013 2 2
S014 2 2
S015 2 2
S016 2 2

~~~~~~~~~~~~~~
Subj vs Level:

H L
S003 2 2
S004 2 2
S005 2 2
S006 2 2
S007 2 2
S008 2 2
S009 2 2
S010 2 2
S011 2 2
S012 2 2
S013 2 2
S014 2 2
S015 2 2
S016 2 2
**** End of data structure information *****
++++++++++++++++++++++++++++++++++++++++++++++++++++

Reading input files now...


** Error:
At least one of the input files has different dimensions!
Run "3dinfo -header_line -prefix -same_grid -n4 *.HEAD" in the directory where
the files are stored, and pinpoint out which file(s) is the trouble maker.
Replace *.HEAD with *.nii or something similar for other file formats.

When I use the command suggested here, I find that all my stats datasets have the same dimensions. I have tried running the 3dLME command on both the "unmasked" stats+tlrc and a "masked" stats+tlrc (having applied each subjects' mask_anat+tlrc to their own stats+tlrc file), but receive the same error message. I have not tried applying the group mask yet. When I view the "unmasked" stats+tlrc file activation is present outside the brain.

Any advice or guidance is greatly appreciated!

Thank you,
Alfonso Alfini
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Subject Author Posted

3dLME error with output from proc.py

Alfonso Alfini March 06, 2016 06:21AM

Re: 3dLME error with output from proc.py

rick reynolds March 06, 2016 11:32PM