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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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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 3 of 3
Pages: 123
Results 61 - 86 of 86
Gang Wrote:
-------------------------------------------------------
> > Oddly enough, the mainF, interaction, and
> intercept results without treating ratings as a
> random effect in
> > the lme command match my results from 3dLME
> while treating ratings as a random effect.
> >
> > Why is this?
>
> Michael, it looks like you could read the mind
by
mrif
-
AFNI Message Board
Gang Wrote:
-------------------------------------------------------
> > lme(values ~ time*treatment +
> ratings,data=lme_data,random = ~1 + ratings |
> subj)
>
> > I get the following error message:
> > nlminb problem, convergence error code = 1
> > message = iteration limit reached without
> convergence (10)
>
> This is basically what 3d
by
mrif
-
AFNI Message Board
Gang Wrote:
-------------------------------------------------------
> > lme(values ~ time*treatment +
> ratings,data=lme_data,random = ~1 + ratings |
> subj)
>
> > I get the following error message:
> > nlminb problem, convergence error code = 1
> > message = iteration limit reached without
> convergence (10)
>
> This is basically what 3d
by
mrif
-
AFNI Message Board
Gang,
Thank you for the feedback.
I'm having some issue trying to replicate the results from one voxel of a whole brain 3dLME analysis in SPSS and exclusively in R.
My model is a 2 factor repeated measures design with 1 within subject varying covariate.
If I try to run the below command in R
lme(values ~ time*treatment + ratings,data=lme_data,random = ~1 + ratings | subj)
by
mrif
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AFNI Message Board
Gang.
Thanks. If not specified with the option "-corStr", what is the default correlation structure that would go into the model. Is it Compound Symmetry?
Also, what type of correlation structures can we select? Is there a list?
How are the glt's handled with 3dLME. Are these standard t-tests that are eventually converted to z-scores? Or is there more involved when constr
by
mrif
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AFNI Message Board
Hello,
In example 2 from the help, there is 1 within-subject factor and 1 within subject quantitative variable.
For example 4 in the help, it mentions obtaining an ICC result with 2 within-subjects factors. What if ICC is of non-interest,and we just want output for the main effect for both factors, interactions, and any specified glt contrasts.
Does the 3dLME allow for 2 within-subjects
by
mrif
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AFNI Message Board
We are seeking a highly motivated candidate with neuroimaging experience for a postdoctoral position at Johns Hopkins University, available immediately or by June 2015. The position involves research on pain, sleep, and reward circuits. The successful candidate will have access to research facilities at JHU and University of Maryland, Baltimore (in collaboration with Dr. David Seminowicz ). The t
by
mrif
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AFNI Message Board
Hello,
When converting dicom files using the to3d option, what is the purpose of the -tpattern option? What exactly is it doing to the data, if anything at all? Or is it just making a note in the header file for later slice timing correction?
Thanks,
Michael
by
mrif
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AFNI Message Board
Gang Wrote:
-------------------------------------------------------
> Hi Michael,
>
>
> > If we take the square root of cov1_r+tlrc, is
> the partial correlation coefficient for covariate
> 1
> > while controlling for covariate 2?
>
> Do the two files give you the same or different
> results? This is what it says in Doug Ward's
> manual
by
mrif
-
AFNI Message Board
Hello,
We are running a multiple regression model using 3dRegana.
We have 2 covariates in the model.
Using the option:
[-rcoef k prefixname] estimate of kth regression coefficient
along with coef. of mult. deter. R^2
is written to AFNI `fith' dataset
We get two separate files: cov1_r+tlrc and
by
mrif
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AFNI Message Board
Gang,
I uploaded the data.
Also, I started running this analysis using the following AFNI version:
Version AFNI_2011_12_21_1014
[]
With the above version, it would not allow me to run the "time*score" model,but I could run the interaction alone, "time:score".
I upgraded the AFNI to the most recent version:
Version AFNI_2011_12_21_1014
[]
With the newe
by
mrif
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AFNI Message Board
Gang,
Just to follow-up, I noticed something with the model I posted for 3dLME. I think the model "time*score" problem is having the same values for the 1st level of time in my model. If I change subject 1's value to 1 and keep the remaining values 0 for level one of Time, then 3dLME executes.
For example:
This works
3dLME -prefix LME_output -jobs 7 \
model "time
by
mrif
-
AFNI Message Board
Gang Wrote:
-------------------------------------------------------
> Hi Michael,
>
> > 1) Having all zeros for visit 1, is this
> possible? Will that cause any problems?
>
> Try it out, and see if the results make sense.
>
> > 2) Is Compound symmetry the default
> covariance-variance structure if you don't specify
> one in the options.
>
by
mrif
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AFNI Message Board
mrif Wrote:
-------------------------------------------------------
> Gang Wrote:
> --------------------------------------------------
> -----
> > I can think of the following: use the two
> values
> > of visit2 - visit1 and visit3 - visit2 from
> each
> > subject as input with the two time intervals as
> > covariate in 3dLME. Follow example 2 in t
by
mrif
-
AFNI Message Board
Peter,
Thanks a great deal.
Switching from Inputfile to InputFile worked.
It is always something so simple.
Michael
by
mrif
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AFNI Message Board
Hello,
I keep receiving the follow message from 3dMVM:
rror in if (len%%wd != 0) errex.AFNI("The content under -dataTable is not rectangular!") else { :
argument is of length zero
Calls: process.MVM.opts
Execution halted
I've tried just about everything as far as changing the code.
Below is my script:
3dMVM -prefix Example -jobs 7 \
-model 'time+sco
by
mrif
-
AFNI Message Board
Rick,
Thank you for the explanation.This helps a great deal.
Michael
by
mrif
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AFNI Message Board
Gang Wrote:
-------------------------------------------------------
> I can think of the following: use the two values
> of visit2 - visit1 and visit3 - visit2 from each
> subject as input with the two time intervals as
> covariate in 3dLME. Follow example 2 in the 3dLME
> HELP. Not sure if that would address your
> question.
>
> Alternatively ignore the time int
by
mrif
-
AFNI Message Board
rick reynolds Wrote:
-------------------------------------------------------
> Hi Michael,
>
> It is important to keep in mind both the
> unmodulated and
> the modulated time series at once. For the
> modulation
> time series, "negative peaks" do not need to be
> negative
> at all in the original data. It just means they
> are below
> the
by
mrif
-
AFNI Message Board
rick reynolds Wrote:
-------------------------------------------------------
> Hi Michael,
>
> By the modulated amplitudes/peaks, do you mean the
> positive
> or negative peaks in the modulation regressor? I
> will make
> that assumption for now.
>
> The mean is subtracted so that the modulation
> regressor
> does not "take away" from the
by
mrif
-
AFNI Message Board
Hello,
I have some questions regarding the stim_AM1 and stim_AM2 option in 3dDeconvolve.
How are the modulated amplitudes adjusted for the resulting stimulus .1D file using the stim_AM2 option? The help information mentions the mean is subtracted from the auxiliary parameter values. Is this why you see negative peaks for some regressors and positive peaks for others? If this is the case, wo
by
mrif
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AFNI Message Board
Gang Wrote:
-------------------------------------------------------
> It's still not clear to me whether you are
> considering Stimulus (with two levels, A and B) as
> an explanatory variable. In other words, are you
> interested in comparing the two stimuli, or do you
> just want to analyze each stimulus type
> separately?
>
Yes, we will want to analyze each
by
mrif
-
AFNI Message Board
Gang Wrote:
-------------------------------------------------------
> Michael,
>
> In addition to the information of three
> measurements per subjects, could you provide more
> information? How many tasks or conditions? How
> many groups? More importantly, what tests or
> hypotheses are you trying to run?
Gang, thanks for your response.
For a given subject=
by
mrif
-
AFNI Message Board
Hello,
We have a question about a repeated measures analysis were are currently running.
All participants conducted scans on 3 separate visits each. Thus, there are 3 measurements per subject.
However, the time in between scan visits varied from subject to subject. For example, the time between visit1 and visit2 is 3 days for subject1, the time between visit1 and visit3 for subject8 is 1
by
mrif
-
AFNI Message Board
Hello,
I have a question regarding missing values and 3dLME.
Take example 3 from the 3dLME -help.
3dLME -prefix Example3 -jobs 24 \
-model "cond*group" \
-ranEff '~1' \
-SS_type 3
by
mrif
-
AFNI Message Board
Page 3 of 3
Pages: 123