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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
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I see. So, If I remove one of the three contrasts it would show me a similar omnibus test? I could use gltCode to compare two groups as well like a post-hoc test, right?
Thank you!
Gang Wrote:
-------------------------------------------------------
> 3dMVM automatically provides an omnibus
> F-statistic for the comparisons among the three
> groups. In addition, your -glfCode sp
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O.M.
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AFNI Message Board
Hi,
Im trying to compare FC of 3 groups using 3dVMV. I tried using this glfLabel below for the F-test, but get the following error: Error in glfRes[]$Df : $ operator is invalid for atomic vectors.
Heres a portion of my script. Could you let me know where the error is?
Thank you.
-bsVars 'group+age+sex+FD' \
-qVars 'age,FD' \
-SS_type 2 \
-num_glf 1 \
-glfLabe
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O.M.
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AFNI Message Board
Sorry again.
>> -model 'Session+Age+Gender' \
>Are you sure that you don't believe there would be no interactions among those 3 variables?
We are trying to account for age and gender on the analysis. How would I create such interactions then? Session*Age*Gender?
>> -ranEff '~1+Session' \
>Change it to -ranEff '~1' \
Wouldn
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O.M.
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AFNI Message Board
>> -model 'Session+Age+Gender' \
>Are you sure that you don't believe there would be no interactions among those 3 variables?
We are trying to account for age and gender on the analysis. How would I create such interactions then? Session*Age*Gender?
>> -ranEff '~1+Session' \
>Change it to -ranEff '~1' \
Wouldn't "~1+Ses
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O.M.
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AFNI Message Board
Hi,
Now I would like to run 3dLME because I have some subjects who have missing data, e.g., some subjects have 2 sessions (baseline and 6 weeks) while others have 3 sessions (baseline, week6, and week16) which would allow me to use more subjects. Also, I wanted it to use because each subject may have a unique intercept (baseline myelin content) as well as a slope (change in myelin from baseline
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O.M.
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AFNI Message Board
Lastly, the sub brick that will tell give me the omnibus F test of session while controlling for age and gender is Age:Gender:Session F brick, correct? See the attached image.
Thank you
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O.M.
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AFNI Message Board
and this will let me look at the effect of session while controlling for the effects of age and gender, correct? Like an omnibus F-test
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O.M.
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AFNI Message Board
It is better to treat "gender" as a factor unless you really know how to dummy-code a categorical variable and interpret the results. Otherwise, you have two genders, so "gender" is a between subjects factor.
> that is true. My bad.
A couple of questions:
1) Do you have missing data?
>No, all subjects have data
2) Do the two genders have substantially diff
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O.M.
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AFNI Message Board
3dLME - 5 years ago
Hi,
I was wondering if my 3dLME model is correct. I am trying to look at changes in myelination from session 1 to 3, while controlling for age and gender effects. I only have one group, so no between-subjects factors.
Thanks.
module load AFNI
module load R/3.2.0-goolf-1.7.20
3dLME -prefix /path_to_dir/myelin_gm-masked.nii \
-mask /path_to_mask/gm_mask_v2.nii \
-model 'Session+
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O.M.
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AFNI Message Board
Hi,
What I did to have the number of distractors vary across trials was to combine both conditions into one stimulus file, so now it looks something like this
67*15 94*25 121*15 166*25 etc
Then I was able to run it without any problems, but this gives me the same result if I just model the two conditions separately and do a glt contrast +east -difficult.
Since I have never worked with
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O.M.
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AFNI Message Board
OK, I see. I did not design this task, so there isn't much I can do. Thanks anyways for the assistance.
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O.M.
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AFNI Message Board
ok. Thanks.
I ran my 3ddecon script and got the following message:
*+ WARNING: -------------------------------------------------
*+ WARNING: Problems with the X matrix columns, listed below:
*+ WARNING: * Column 6 is all zeros
*+ WARNING: * Column 8 is all zeros
*+ WARNING: -------------------------------------------------
*+ WARNING: !! in Signal+Baseline matrix:
* Largest s
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O.M.
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AFNI Message Board
I have one additional question: If I wanted to get the linear relationship between regional signal changes and number of distractors, would I have to make an additional glt, e.g., +easy[1] +difficult[1] or the +easy[1] -difficult[1] glt will give me that?. I would like to get clusters in the brain that indicate signal change going up as the number of distractors goes up as well.
Thanks a lot.
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O.M.
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AFNI Message Board
>What variable are you trying to use to correlate with (or modulate) the individual trials? Some behavioral measure?
No, I would like to use the number of distractors to modulate the individual trials, e.g., one condition (easy) has 15 distractors, while the second one (difficult) has 25 distractors.
>You put that measurement after each asterisk (*). You may use 1dMarry to combine the
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O.M.
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AFNI Message Board
Hi Afni experts,
I am attempting to run a parametric modulation analysis. There is some old data sitting here where participants were responsable for finding a target letter surrounded by several distractors, and there were 2 conditions: easy and difficult, with difficult having more distractors than the easy condition.
How do I set up my 3ddecon script for such analysis? I know I have to u
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O.M.
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AFNI Message Board
Wow, thanks a lot.
I will give all this a try and see how everything turns out. I will most likely be doing comparisons between 2 groups: patient vs. healthy control.
Again thanks
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O.M.
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AFNI Message Board
Dear AFNI people,
I've been playing around with some DTI data and found this preprocessing pipeline from a blog by Peter Molfese. I have run the following steps:
Correct Eddy Distortions
3dAllineate -base 'dwi+orig.HEAD[0]' -input 'dwi+orig.HEAD' \
-prefix dwi_al -cost mutualinfo -verb -EPI
Step 2: Fit Tensors using a nonlinear fitting
3dDWItoDT -prefix te
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O.M.
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AFNI Message Board
Yeah, that was my thought too, but I ran a quick script that puts the files in the correct sequence and still gave me that output. I used dicm2nii.m for this and it was fine. I just wanted to run it as a script for all my subjects because for dicm2nii.m you need to do each subject manually.
Thanks
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O.M.
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AFNI Message Board
Hi,
I was trying to reconstruct my T1 images from dicom format and used to3d, however the images look odd (https://www.dropbox.com/s/nb8g6bhosrzkmgt/Screenshot.png?dl=0).
I used a pretty simple line of code to run this, but maybe I need to add an extra flag, which I did and still does not look ok.
to3d -session ${subjectsDirectory}/${subj} -prefix ${subj}_anat.nii.gz 'image_*'
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O.M.
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AFNI Message Board
I think I know where I messed up. When I selected both path coef. and t-values for group analysis, the t-values are only for the instantaneous effect. If I select only the path coefficients for group analysis, it works fine.
Thanks for all your help
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O.M.
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AFNI Message Board
Also, I just tried this and gave me this error when trying to do group analysis
Lapack routine dgesv: system is exactly singular: U[1,1] = 0
This is my instantaneous effect specification matrix
visual dorsal ventral
visual 0 0 0
dorsal NA 0 0
ventral NA NA 0
Thanks again
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O.M.
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AFNI Message Board
ok, thanks.
One last question.....When it tells me to save my path matrices at the end, it gives me 3 options (with a lag of 1, 2, and 3). I tried to read your paper but its way beyond my understanding in math (equations and stuff), which path matrix would give me the best model. What I did for my data was I ran 3dDeconvolve to remove any drift effects, motion, linear trends, etc without model
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O.M.
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AFNI Message Board
I noticed that I can't model all possible connections, e.g., A, B, and C I can only model 3 connections because of the n(n-1)/2 formula. If I want to check all possible connections, would you suggest doing something like A=>B A=>C, B=>A B=>C, and C=>A C=B and then use that to get like an overall summary of all the connections.
That's why I liked 1dSEM, because one coul
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O.M.
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AFNI Message Board
Thanks!
I played around with it and it worked for 1 subject, but I have 22 so it should keep me busy for a while
I will probably ask more questions as I keep using it
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O.M.
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AFNI Message Board
Hi,
You probably missed my previous message, but I had one quick question. I came across your 1dSEM tcsh script and tried it using 3 rois. My output yielded path coefficients within the -8 and 8 range. Maybe I ran something wrong because most of the papers I've seen report within the -1 1 range. For the script, I took the left column (++ left vectors) of each ROI SVD files and then grabbe
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O.M.
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AFNI Message Board
Dear AFNI people,
I recently run into your 1dSEM tcsh script and played around with it for a while. I ran the tree growth search model (didnt really have a particular model, so I decided to let 1dSEM to find the best model) using 3 roi's and it gave me path coefficients around 8 and -8. Is this possible? Also, what does cost and Akaike's Information Criterion mean? how can I get root
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O.M.
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AFNI Message Board
Hi,
I'm attempting to run an analysis where I'm interested in looking at the relationship between fcmri z-scores and behavioral data (sort of a whole-brain correlational analysis). I first ran 3dTcorr1D and that worked beautifully, however I forgot to covary for verbal IQ. Then, I decided to use 3dRegAna for this analysis (relationship between fcMRI and behavioral scores while removi
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O.M.
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AFNI Message Board
Ok, I attached the image. If not, I copy/pasted a dropbox link to the image.
Dropbox link
Thanks
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O.M.
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AFNI Message Board
> To be clear, you seem to be describing a paired t-test here. Did you run 3dttest++ with the -paired option?
I think I should have started from here. On my 3ddeconvolve script for each participant, I had 4 trials with their respective timing information. Then on the GLT flag, I combined 2 trials (A) and combined the other 2 trials (B) and made the contrast A - B. Please, see below
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O.M.
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AFNI Message Board
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