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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
Page 2 of 3
Pages: 123
Results 31 - 60 of 86
Thank you both for your input.
It helped a great deal.
Michael
by
mrif
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AFNI Message Board
Thank you both for the responses.
I have 2 questions:
1) If I use 3dRegAna or 3dTcorr1D, is it necessary to center my behavior measures? If so, why?
2) If I use 3dttest++, why do I have to standardize both fmri and behavior measures?
Thanks,
Michael
by
mrif
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AFNI Message Board
Hello, we want to correlate behavior measures with our fmri data.
We've used 3dRegAna in the past, but could we also use 3dttest++? Is using 3dttest++ a better way to run the correlation?
If so, how do we set it up to use 3dttest++?
If we include the -setA as the imaging set and -covariates as the behavior measure set, how do we get the output as an r value?
Thanks,
Michael
by
mrif
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AFNI Message Board
Gang Wrote:
-------------------------------------------------------
> Michael,
>
> > What if you want create a 2-way model, but both
> factors are within subjects.
>
> For a two-way within-subject ANOVA without missing
> data, simply use 3dANOVA3 -type 4 or 3dMVM.
>
Okay, great.
> > How would the model setup differ from Example 3?
> Would i
by
mrif
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AFNI Message Board
Hello,
In example 3 for 3dLME, it has a 1 within-subjects factor and 1 between subjects factor.
What if you want create a 2-way model, but both factors are within subjects.
How would the model setup differ from Example 3? Would it be the same as Example 4, but without the ICC option?
Additionally:
What is the factor limit for 3dLME? Can it handle 3 or 4 factors within a model?
by
mrif
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AFNI Message Board
Hello,
I recently starting using uber_subject.py after using afni_proc.py in the past.
It seems uber_subject.py is more of a starting point to generate a processing script. It doesn't appear to have as many options available as afni_proc.py. Is that truly the case?
Just curious because the gui is very helpful when trying to organize all of the processing options as opposed to gene
by
mrif
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AFNI Message Board
ptaylor Wrote:
-------------------------------------------------------
> They are files that hold AFNI and SUMA environment
> variable settings; those files hold a lot of nice
> defaults, and then you can add/subtract/modify
> them as you wish.
>
I see. Do I lose anything by not copying this to a ~/.afnirc . All our paths, environment variables are setup in our .cshrc fil
by
mrif
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AFNI Message Board
Hello,
What are the purposes of the .afnirc and .sumarc files?
When I run the command:
afni_system_check.py -check_all
I see this in the summary:
* consider running: cp /installed/AFNI/bin/AFNI.afnirc ~/.afnirc
* consider running "suma -update_env" for .sumarc
Additionally, looking at the suma -help options, it makes reference to installing suma template data
by
mrif
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AFNI Message Board
Yes, the 3dClustSim results were done without including the blur option.
Which leads me to another question regarding the -acf option in 3dClustSim:
The values you get from the -acf option are from 3dFWHMx, correct?
However, my preprocessing was done in SPM on resting state data, and then we ran a group ICA analysis on the preprocessed datasets. There is no errts file I could find in th
by
mrif
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AFNI Message Board
Hello,
We have a question regarding 3dClustSim and the mask used for processing.
In the past we would make a group mask for group analysis. The analysis was conducted in tlrc space.
But I recall in the past it was recommended to resample the group-mask voxel size to the orignal space voxel size before running AlphaSim:
"As data are acquired in original voxel size, do make sure th
by
mrif
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AFNI Message Board
Hello,
Which program should I use if I want to see how correlated an Independent component z-map is spatially correlated with the, for example, the default mode network z-map map from Smith et al 2009.
I noticed using both yields similar results.
Also, what purpose does the -demean option server in 3ddot? Is it necessary?
Michael
by
mrif
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AFNI Message Board
Gang,
Is it possible to upload the data and have you take a look at it?
Michael
by
mrif
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AFNI Message Board
Gang,
Thank you for your response.
Yes, now running the post-hoc tests for;
scan1_Group1_vs_Group2
scan2_Group1_vs_Group2
using independent t-tests, I get the same results as 3dMVM. However if I do paired t-tests I get different results from:
group1_Scan1_vs_Scan2
group2_Scan1_vs_Scan2
Is this because of the degrees of freedom? Its only 12 (13 subjects) If I run the pair
by
mrif
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AFNI Message Board
Gang,
Hello, I've run with this dataset and ran into an issue where calculations in R and SPSS didn't match.
I ran my 2 x 2 mixed model using 3dMVM
Here is the breakdown:
2 Factors:
group - between subject 2 levels (with, without)
scan - within subject 2 levels (pre, post)
We generated a group x scan interaction map and looked at the interaction post-hoc comparisons
by
mrif
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AFNI Message Board
Hello,
I have a question regarding regress_censor_motion LIMIT in afni_proc.py?
What exactly is the LIMIT value? Does it reflect mm or degrees? The amount of excessive rotation/translation in degrees/mm?
Any help would be appreciated.
Thank you.
MIchael
by
mrif
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AFNI Message Board
Gang,
I uploaded the data and sent you an email.
Thanks again.
Michael
by
mrif
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AFNI Message Board
Gang, I made the change and I'm still getting an error.
I updated my AFNI to the 08_25_15 build. Still the same error message.
I suspect it is something wrong with my contrast (s), because if I just run it without any glt's, the program starts to run.
Here is my setup now:
3dMVM -prefix MVM_results -jobs 4 \
-bsVars 'group' \
-wsVars 'run' \
-ma
by
mrif
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AFNI Message Board
Gang,
Thank you for your response.
I keep getting the following error message:
** Error:
Incorrect level coding in variable group : group2
Here is my setup:
3dMVM -prefix MVM_results -jobs 4 \
-bsVars 'group' \
-wsVars 'run' \
-mask group_mask.nii \
-num_glt 5 \
-gltLabel 1 group_by_run_interaction -gltCode 1 'group : 1*group1 -1*group2
by
mrif
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AFNI Message Board
Hello,
EDIT:
How does one setup a 2 x 2 Mixed ANOVA with 3dMVM.
The main reason to use MVM is because the samples for the between subjects factors are unbalanced.
Here is the setup:
1 within factor: 2 levels
1 between subjects factor: 2 levels
I want to test the main effects for factor 1 and the main effect for factor 2.
And also, we want to test the interaction betwee
by
mrif
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AFNI Message Board
rick reynolds Wrote:
-------------------------------------------------------
> Hi Milael,
>
> I believe it is libxp6 on ubuntu. So try:
>
> sudo apt-get install libxp6
>
> or, to get additional needed packages:
>
> sudo apt-get install tcsh libxp6 python-qt4
> r-base
>
> - rick
Thanks rick
sudo apt-get install libxp6
The command above
by
mrif
-
AFNI Message Board
Hello,
I'm trying to install AFNI linux_openmp_64 on Ubuntu 14.04.2 LTS.
When I try to use the command afni, I get the following error message:
/afni: error while loading shared libraries: libXp.so.6: cannot open shared object file: No such file or directory
Any help would greatly be appreciated.
Thank you.
Michael
by
mrif
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AFNI Message Board
ziad Wrote:
-------------------------------------------------------
> Hello Michael,
>
> That's my bad. I will fix this soon, I hope.
>
> cheers
> Ziad
Ziad,
Thank you for your response.
If it helps any, I forgot to mention I'm using linux_openmp_64 on Ubuntu 10.04.
Thanks again.
Michael
by
mrif
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AFNI Message Board
Hello,
While using the the AFNI viewer, when I select an underlay and overlay, increase the montage rows/columns,etc. the following message keeps appearing with each click on the viewer in my terminal window:
No support for non-zero filling for short errorNo support for non-zero filling for short errorNo support for non-zero filling for short errorNo support for non-zero filling for short
by
mrif
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AFNI Message Board
Gang Wrote:
-------------------------------------------------------
> > What is the calculation for the standard
> deviation of the estimator?
>
> Michael, in this context the standard error of the
> estimator is not good enough for you? The standard
> deviation is usually used to show how spread the
> samples are, but in other occasions the two
> phrases are
by
mrif
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AFNI Message Board
Gang Wrote:
-------------------------------------------------------
> Michael,
>
> The formula I provided before is for the standard
> error of the estimator:
>
> beta divided by t (or z)
Thank you for the clarification.
What is the calculation for the standard deviation of the estimator?
Michael
by
mrif
-
AFNI Message Board
Gang Wrote:
-------------------------------------------------------
> Michael,
>
> > This is referring to standard deviation,
> correct? Additionally, How would you calculate the
> standard error?
>
> Regarding standard deviation vs. standard error:
> standard deviation usually refers to the extent of
> how spread or concentrated the data (or samples)
&
by
mrif
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AFNI Message Board
Gang Wrote:
-------------------------------------------------------
> 3dLME currently does not handle missing data at
> the voxel level. If the value is 0, 3dLME simply
> takes it at face value.
>
Gang, thanks. Will definitely take that into consideration.
> > is there a way to generate Standard
> deviation/Standard error for the mean value
> > of a factor
by
mrif
-
AFNI Message Board
Gang Wrote:
-------------------------------------------------------
> > I'm confused because I thought Mixed Models can
> handle missing timepoints within
> > a dataset. If a repeated measures design has 3
> levels, and one of the levels is
> > missing (NA), wouldn't the model still include
> the other 2 timepoints? Not omit them?
>
> If one su
by
mrif
-
AFNI Message Board
Page 2 of 3
Pages: 123