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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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Hello,
We have a dataset with 3 factors: 2 within subject factors (Pain, Faces), 1 between subjects factor (Group),
A 2 x 3 x 2 design.
Factors: Pain (Levels: pain, nopain)
Faces (Levels: neutral, positive, negative)
Group (Levels: patients, controls)
Here is our setup
3dLME -prefix result-lme_group -jobs 10
by
mrif
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AFNI Message Board
Thanks Gang.
We want to simplify our model and only include 1 qvar, weight.
The model would then be: -model 'time*weight'
To investigate the investigate the effect of the interaction, we would compare the slopes for weight at each level of time, correct?
-gltlabel 1 'weight_ V1-V2' -gltcode 1 'Time: 1*V1 -1*V2 weight : '
-gltlabel 2 'weight_ V1
by
mrif
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AFNI Message Board
Hello,
We have within-subject design where participants are scanned on multiple visits (4 times per participant). Time between visits is 2 years. Some visits are missing for a few participants. We'll call this variable 'time'.
We also collected two quantitative variables ("weight", "age") during each visit, so we have two time-variant covariates to add t
by
mrif
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AFNI Message Board
Hello,
Is there an option to specify the correlation structure of the residuals with 3dLMEr as it was with the older 3dLME?
Thanks in advance.
by
mrif
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AFNI Message Board
Dainel,
Thanks for the feedback. Yes, we were attempting to install on Ubuntu 18.04, but mistakenly used the linux_openmp_64 package as we used with Ubuntu 14.04.
After installing with the linux_16_64 package, AFNI now works, and we start the application successfully.
Thanks for your help.
Michael
by
mrif
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AFNI Message Board
Hello,
Ran into an issue after installing AFNI on Ubuntu 18.04.
I receive the following error when calling afni:
error while loading shared libraries: libXp.so.6: cannot open shared object file: No such file or directory
Any help would be appreciated.
Thanks.
Michael
by
mrif
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AFNI Message Board
Gang Wrote:
-------------------------------------------------------
> > Can 3dLME handle missing data in the case where
> a subject may have a beta coefficient, but a
> missing behavioral measure covariate, and vice
> versa?
>
> No, it cannot.
Thanks.
1. Is there a possible workaround to achieve something like it?
2. Can 3dLME handle 2 continuous within-sub
by
mrif
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AFNI Message Board
Hello,
I have a question regarding missing data and 3dLME.
Can 3dLME handle missing data in the case where a subject may have a beta coefficient, but a missing behavioral measure covariate, and vice versa?
Thanks.
Michael
by
mrif
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AFNI Message Board
Gang Wrote:
-------------------------------------------------------
> There are a couple of possibilities for the
> discrepancies between 3dMVM and 3dLME.
>
> 1) If one quantitative is quite skewed among the
> subjects, that may have a large impact,
>
> 2) The way 3dLME counts the degrees of freedom is
> slightly different from 3dMVM, and the impact
> could
by
mrif
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AFNI Message Board
Gang,
Running 3dLME with or without the missing subject produces similar results. Both of those results differ dramatically from the 3dMVM output.
I'm not sure if it is just the nature our data set and the number of factors/levels included in the model.
Do you mind if I upload the data for you to take a look at it?
Thanks.
Michael
by
mrif
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AFNI Message Board
Gang,
Thanks for your response.
We are running a 4 x 3 x 3 model. All within subjects factors.
3 Factors:
Visit: 1, 2, 3 4
Temp: 1 2 3
Trial: 1 2 3
We do have missing data for 1 subject. That subject has missing data from 1 visit. They only have data from 3 out of 4 visits.
In addition to the random effects question, there is something else:
We've run this model witho
by
mrif
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AFNI Message Board
Hello, we are running a 3-way repeated measures anova
In our original setup for 3dLME we ran:
-model 'factor1*factor2*factor3'
-ranEff '~1`
Where the intercepts are the random effect.
However, what if we want to include factor1 also as a random effect? What is the proper setup?
If we take out factor1 in the model in command and place it in the ranEff command, how
by
mrif
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AFNI Message Board
Thanks for the feedback Rick.
I have another question. Does duration modulation only pertain to BLOCK?
What about if I"m using the TENT model? How would that work.
Thanks.
Michael
by
mrif
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AFNI Message Board
Hello,
I've been looking at the ideal functions resulting from 3dDeconolve, and was quite puzzled at the length of each trial.
Here is an example:
3dDeconvolve -nodata 195 2.0 -num_stimts 1 -polort 3 -x1D example-X.xmat.1D \
-stim_times 1 '1D:112 168 322' 'BLOCK(14)'
Now, the TR here is 2. Since the X.xmat.1D files are in TR's, I expected to see a
by
mrif
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AFNI Message Board
Rick,
I just wanted to follow-up regarding this question:
Thanks.
Michael
by
mrif
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AFNI Message Board
Rick,
Thanks for the response. Is there any advantage to letting the amplitude vary vs. using the same peak amplitude of 1 with dmBLOCK(1) or dmUBLOCK(1)?
Also, Rick, I'm including this in a setup for afni_proc.py. I'm a little confused on how to set this up looking at Example 7 for afni_proc.py.
Say if I have "3 types of pizza". Would it look something like this?
by
mrif
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AFNI Message Board
Hello,
I have a question including different durations for each block in an fmri run using 3dDeconvolve (or even afni_proc.py)
The run has 10 trials. 8 trials are 15 seconds in duration.
For this particular run, the majority of the blocks are of the same duration, 15 seconds. For 2 trials, there was a machine malfunction where the stimuli was too short,12 seconds,and too long, 17 seconds
by
mrif
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AFNI Message Board
Hello,
I have some more questions regarding the dataset input to use.
It is recommended to use the errts file from 3dDeconvolve.
When using the errts file, is it necessary to include the -detrend option?
Is the errts file the most ideal dataset to use for 3dFWHMx? Or is it the final preprocessed functional data with the -detrend option?
Thanks,
Michael
by
mrif
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AFNI Message Board
Gang Wrote:
-------------------------------------------------------
> OK, my bad! I forgot to add a space right after
> "condition":
>
> -gltLabel 1 LinearTrend -gltCode 1 'condition : '
Gang,
I tried the above line, and now get the following message:
** Error:
Inappropriate coding in test No.1!
Here is the setup:
3dLME -prefix file_r
by
mrif
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AFNI Message Board
Gang Wrote:
-------------------------------------------------------
> > I get the following error message:
>
> The test index should be added:
>
> -num_glt 1 \
> -gltLabel 1 LinearTrend -gltCode 1 'condition: '
> \
>
Gang, I included those lines and still get the same error message:
Error in `[.data.frame`(dataStr
by
mrif
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AFNI Message Board
Gang Wrote:
-------------------------------------------------------
> You can try the following:
>
> 3dLME -prefix ... -jobs 12 -model
> "condition*treatment" -qVars "condition" -ranEff
> '~condition' \
> -gltLabel LinearTrend -gltCode 'condition: ' \
> -dataTable \
> Subj condition treatment InputFile \
> s1 -1 befo
by
mrif
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AFNI Message Board
Gang Wrote:
-------------------------------------------------------
> > Is there another way to construct the linear
> trend without excluding the middle term? Could
> using 3dRegAna work?
>
> No, forget about 3dRegAna. 3dLME might be a better
> solution. First, code "condition" as a
> quantitative variable:
>
> one -> -1
> two -> 0
by
mrif
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AFNI Message Board
Gang Wrote:
-------------------------------------------------------
> Michael,
>
> Your case 1 essentially only compares "one" and
> "three", which would show whether "one" and
> "three" differ from each other. To obtain brain
> regions with "one > two > three", go with your
> case 2.
Okay, I'm still a s
by
mrif
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AFNI Message Board
Gang Wrote:
-------------------------------------------------------
> Matthew,
>
> Add two more tests:
>
> -gltLabel 4 grp_task_1vs2 -gltCode 4 "group : -1*
> healthy 1* diseased strategy : 1*task_1 -1*task_2
> " \
> -gltLabel 5 grp_task_2vs3 -gltCode 5 "group : -1*
> healthy 1* diseased strategy : 1*task_2 -1*task_3
> " \
>
&
by
mrif
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AFNI Message Board
Hello,
I have a question regarding linear contrasts output from 3dMVM in comparison to output from 3dttest++
I have a 2x3 within subject design.
factor1: with 2 levels= pre, post
factor2: with 3 levels= one, two, three
We ran 3dMVM and setup several glt tests. One of the tests involved collapsing across 3 levels for Factor2 for level pre of Factor1
-gltLabel 1 'pre_Factor1
by
mrif
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AFNI Message Board
Page 1 of 3
Pages: 123