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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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Hi,
I am doing an analysis of activation using 3dMVM and have differences in volume of a subcortical structure that I would like to control for.
Do I demean the volume measures before entering them in the analysis or I don't need to do that and can just enter volume measures?
thank you!
by
katya.dobryak
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AFNI Message Board
Hello,
I ran small volume correction using 3dClustSim on an anatomical ROI identified based on prior literature. Then, I used the output of 3dClusSim in Clusterize to threshold my activation map.
I have the following question:
How can I view the statistical map that shows only the active voxels from my ROI.
Thank you for your help.
by
katya.dobryak
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AFNI Message Board
i have the latest version. It's so strange, because the program runs if i just include 2 factors and not 3 factors. For example, I am able to run the script without group being a factor, with just apathy x trial type and without apathy with just group x trial type.
by
katya.dobryak
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AFNI Message Board
I changed it to
-model "group*apathy" \
-wsVars 'trialtype' \
by
katya.dobryak
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AFNI Message Board
hm. changing it to a between subject variable didn't help. Same thing shows up
by
katya.dobryak
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AFNI Message Board
Sure.
Loading required package: afex
Loading required package: coin
Loading required package: survival
Loading required package: splines
Loading required package: car
Loading required package: MASS
Loading required package: nnet
Loading required package: lme4
Loading required package: Matrix
Loading required package: lattice
Attaching package: \u2018lme4\u2019
The following object
by
katya.dobryak
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AFNI Message Board
hi, my 3dmvm fails due to model test failure. Basically, I have one between-subs factor and two within-sub factors. My model specification is presented below. Would appreciate any ideas about how it can be changed.
3dMVM -prefix Apathy -jobs 24 \
-model group \
-wsVars 'trialtype*apathy' \
-num_glt 3 \
-gltLabel 1 tbi_apathy_high-low -gltCode 1 'group : 1*tbi apathy : 1*hig
by
katya.dobryak
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AFNI Message Board
hi, I have two questions.
1) I want to use accuracy as a covariate in my MVM/LME. Is LME a better analysis for that or can I still use MVM?
2) is the format for the covariate file the same as for 3dttest and 3dMEMA?
Thanks!
by
katya.dobryak
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AFNI Message Board
Does 3dMVM take nifti files?
i am getting an error indicating that the dataset cannot be loaded, though I can run 3dAnova.
thanks!
by
katya.dobryak
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AFNI Message Board
Hi, I just wanted to double-check whether I am doing the right thing.
I have variable trial duration in the experiment, so in my 3dDeconvolve I need to use dmBLOCK(1),where 1 is the amplitude, with stim_times_AM1 , correct?
In the stim_times file I have the following format: 'time : trial duration'.
Thank you!
by
katya.dobryak
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AFNI Message Board
the problem was with the spaces. So now it is working.
by
katya.dobryak
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AFNI Message Board
I tried 'GAM(8.6,.547,1)' but that doesn't work either.
by
katya.dobryak
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AFNI Message Board
Hi,
i want to indicate in my deconvolve script the duration of the stim, which is 1 second.
Putting this, as i did with SPMG1, didn't work:
-stim_times 07 ./1d_files/control.1D 'GAM (1)'
So i am wondering what is missing .
thank you!!
by
katya.dobryak
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AFNI Message Board
Hi,
I was wondering whether in 3dMVM I can collapse across the levels of one of the conditions in order to contrast it to a different condition that has only one level.
I have the following design: a neutral feedback condition and a non-neutral feedback condition that has 2 levels, i.e. positive and negative feedback.
3dMVM -prefix neutral_non-neutral\
-model "group*condition&quo
by
katya.dobryak
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AFNI Message Board
Aha, yes. now i only get this:
Error in dim(inData) <- c(dimx, dimy, dimz, NoFile) :
dims do not match the length of object [35159308]
by
katya.dobryak
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AFNI Message Board
3dMVM - 10 years ago
Hi Gang,
I am running 3dMVM again but on a different sample.
I am getting silly errors, and i am sure that some of them due to me mistyping something or having an extra space where i don't need it. can you please take a look?
Here are the error messages.
** Error:
Incorrect level coding in variable Group : 1
Error in dim(inData) <- c(dimx, dimy, dimz, NoFile) :
dims do
by
katya.dobryak
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AFNI Message Board
I do define them at the beginning of the script and both variables are being echoed.
by
katya.dobryak
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AFNI Message Board
Hi! Thanks so much for looking at this. I am not sure whether the error is related to the fact that I am including sub-bricks or not. Maybe the matrix that I have in the dataTable has an empty cell..?
--
3dLME -prefix nback_MS_output \
-jobs 4 \
-model "Task*Group*Time" \
-ranEff '~1' \
-SS_type 3 \
-num_glt 6 \
-gltLabel 1 '2back-1back' -gltCode 1 'T
by
katya.dobryak
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AFNI Message Board
3dLME - 10 years ago
Dear afni community,
I am trying to run3dLME and watned to double check whether sub-bricks can be used in the data table. More importantly, I keep getting an error indicating that "-dataTable is not rectangular". What does that specifically mean and how to I fix that?
Thank you!!
by
katya.dobryak
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AFNI Message Board
Hi, I was reading the post and until now was not confused. But now I am confused about the ttest output with the covariate.
Gang, what do you mean by the 'effect of covariate'?
As far as I understood, the sub-brick with the covariate shows results with a covaried variable controlled for. So, for example, if I want to compare two groups with and without depression, the first two sub-
by
katya.dobryak
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AFNI Message Board
Hello AFNI community,
I ran 3dMEMA (between-groups, 1 coefficient) for the first time and trying to understand the output of it. Can anyone please tell me where to find out what the contrast options mean, such as tau^2 and QE?
Thank you!
by
katya.dobryak
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AFNI Message Board