Show all posts by user
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
Page 1 of 1 Pages: 1
Results 1 - 17 of 17
Hi All,
I am trying to run 3dANOVA with 4 levels. The program runs great with ~945 participants, however, I would like to run the program on 2,000 participants. When I try running 3dANOVA on all of my participants, I receive the error: ** FATAL ERROR: Program 3dANOVA: too many data files. I did try using the -@ option (getting rid of all \), which works to fix this issue for 3dttest++, but th
by
bfair
-
AFNI Message Board
I found the issue! Problem resolved and -@ does work on my larger datatset.
Best,
~B
by
bfair
-
AFNI Message Board
Hi Rick,
I am not confident that the -@ fixed my problems on the previous script. And I am running into the same issue on a current 3dttest++ with 1,800 participants using a functional dataset. The script will only run on around 1,400 participants before I receive the error "argument list too long." If I use -@, I receive an error reading "cannot load dataset." The script
by
bfair
-
AFNI Message Board
Hi Rick,
I updated my binaries and Bob's change seems to have fixed the problem. I am now problem-shooting some other errors, but I will let you know if I run into this argument error again.
Thank you for all of your help.
Best,
~BFair
by
bfair
-
AFNI Message Board
Hi all,
I am trying to run a 3dttest, however, I keep getting the following error: 3dttest++: Argument list too long. How to I fix this issue? I am running the script on a Mac El Capitan with updated versions of R and AFNI (Sept 4th). An example of my script is below- However, instead of 2 subjects, I have 2,000.
3dttest++ -overwrite \
-setA GroupA \
000000022453 /Users/bfair/Documents/
by
bfair
-
AFNI Message Board
Hi All,
I am new to AFNI and this is my first AFNI download. I am using El Cap on Mac version 10.11.6. Additionally, R is up-to-date and I have dowloaded xQuartz and xcode as per the instructions on:
However, when I enter brew doctor into the terminal I get a slew of warnings:
Brittanys-iMac:~ brittanyfair$ brew doctor
Please note that these warnings are just used to help the Homebrew
by
bfair
-
AFNI Message Board
Hi Gang,
Updating the operating system and AFNI version did fix this issue.
Thank you for all of your help.
~BFair
by
bfair
-
AFNI Message Board
Hi Gang,
medlocals-iMac:Test_Folder Catherine$ afni -ver
Version AFNI_2011_12_21_1014
[]
Do you think this could be the issue?
Best,
~BFair
by
bfair
-
AFNI Message Board
Same error message when -jobs 1 is removed:
** Error:
Expecting 1 parameters for option "-prefix".
Have 3 parameter(s) in string "test.nii -bsVars bob" instead.
NOTE that -bsVars in bad option above is not a recognized option.
** Error:
Error parsing arguments. See 3dMVM -help for details.
The script I used:
3dMVM -prefix test.nii \
-bsVars
by
bfair
-
AFNI Message Board
Hi Gang,
Thank you so much for your response. I altered my quotations like you suggested without luck. I still receive this error:
** Error:
Expecting 1 parameters for option "-jobs".
Have 3 parameter(s) in string "1 -bsVars bob" instead.
NOTE that -bsVars in bad option above is not a recognized option.
** Error:
Error parsing arguments. See 3dMVM
by
bfair
-
AFNI Message Board
Hi Gang,
Thank you for your response. The variables listed as 0's and 1's are categorical (they dictate the site of data collection), thus I did not list them under qVars. Do I need to list them as a factor somehow?
Also, I am only interested in the covariate effect of my quantitative variables, so I believe I do not need to center them.
I thought my quantitative variables w
by
bfair
-
AFNI Message Board
Hi Gang,
Thank you so much for your suggestion. I have made the change, however, I am receiving a new error now.
Script:
3dMVM -prefix test.nii -jobs 1 \
-bsVars ‘bob’ \
-dataTable \
Subj bob InputFile \
000000022453 2.000 s888mwc1mprage000000022453.nii \
000000075717 2.000 s888mwc1mprage000000075717.nii \
000000106601 1.000 s888mwc1mprage000000106601.nii \
000000106871 1.000 s8
by
bfair
-
AFNI Message Board
Hi Gang,
Yes, latent_class is a subject-grouping variable. I do have more subjects...but I wanted to make sure the script would run with fewer subjects before adding the rest. I would like to refrain from using multiple independent T-tests in order to avoid Type I errors. Any idea on how to fix this error to use 3dLME?
Best,
~BFair
by
bfair
-
AFNI Message Board
Hi Gang,
Bob is a categorical variable (1 through 4) and it should be a between subjects factor as that is the variable of interest for my univariate ANOVA. Bob = latent class, but 'class' is a command in R, so I just changed the name to something silly to not run into any parsing errors.
Best,
~BFair
by
bfair
-
AFNI Message Board
Hi all,
I am trying to run a basic ANOVA using 3dMVM. When I attempt to run the script, I get an accurate summary of data structure, however, the script 'errors out' after reading the input files. My error is as follows:
Reading input files now...
~~~~~~~~~~~~~~~~~~~ Model test failed! ~~~~~~~~~~~~~~~~~~~
Possible reasons:
0) Make sure that R packages afex and phia have bee
by
bfair
-
AFNI Message Board
Hi,
I am trying to run a 3dLME script (simple ANOVA) with my variable for comparison being 'latent class.' I keep getting the following error:
Error in `[.data.frame`(lop$dataStr, , jj) : undefined columns selected
Calls: process.LME.opts -> [ -> [.data.frame
Execution halted
My script is as follows:
3dLME -prefix test -jobs 1 \
-model "latent_class+bl_comple
by
bfair
-
AFNI Message Board