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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!
apologies in advance for double posting! We are working on a gPPI analysis and wanted to verify we have the right interaction regressors.
For obtaining the interaction regressors, this is what is first suggested:
'First create a 1D (one column) file, conditionA.1D, with 0's (at those TR's where condition A does not occur), 1's (at those TR's where condit
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prerona
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AFNI Message Board
Hi Rick
I have a question on this topic. How do we determine if the stimulus onset times are synchronized with TR grids
best wishes
Prerona
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prerona
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AFNI Message Board
That did fix the problem! I am so sorry - I didn't spot that
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prerona
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AFNI Message Board
Hi
please could you help me - I am try to run 3dDeconvolve (command pasted below) with -stim_times_AM2 option but getting an error reading the stimuli file (see below). I have copied the contents of the stimulus file at the end. I also tried using file_tool seeing what Rick said to someone else in another thread but didnt shed any light (pasted output below).
Thanks for any advice
Since
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prerona
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AFNI Message Board
I included some brain images in a publication which show "heatmaps". However, we got a reviewer comment asking for color-bars to make it easier to interpret effect size or show "across contrasts, what does a particular shade of yellow mean". Does anyone have any suggestions regarding how we can do this?
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prerona
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AFNI Message Board
Thank you so much for your help!
I have run the 3dLME command as below and then done clusterize with NN1 and then I opened the cluster report window to see the list of clusters. Here the XYZ location option is set to Peak. Everything else is set to default.
3dLME -prefix ${output} -jobs 5 \
-model 'Dx*Direction*Number*Age' \
-ranEff '~1' \
-SS_type 3 \
-num_glt 8
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prerona
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AFNI Message Board
Hi
the difference in cluster volume is not big - the f test cluster size is 567 ( with peak coordinates as -34 38 -36) and for the GLT it is 586 ( with peak coordinates as -36 34 -36 )
The F-stat values are equal to the t-stat squared
"For the GLT result, are you get the peak of what: effect estimate or t-stat? " - I am not sure how to check this?
Thank you!
Prerona
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prerona
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AFNI Message Board
Hi
I have 2 questions about my 3dLME analysis. I have pasted the code below
1) When I look at the GLT 1 "ADHDvTD_BackvForw", my resulting clusters are slightly different in peak and cluster size from the F Test between the same factors Diagnosis X Complexity - though the p threshold is the same. Please could someone help me understand why these are different and which one is more
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prerona
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AFNI Message Board
Hi
I found this thread that answers one of my doubts and thank you very much for this. I just wanted to ask what is the number 3.1 in the command
3dclust -1Dformat -nosum -1dindex 10 -1tindex 11 -2thresh ? ? -dxyz=3 3.1 X
Also, can -1dindex & -1tindex be same (as in an F test)
Thank you so much for your help!
Sincerely
Prerona
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prerona
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AFNI Message Board
The difference between one and two is just that one is inverse of 2. In our case though I ran all 3 analysis and my results are the same - so I guess that is good!!!
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prerona
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AFNI Message Board
Thank you! Realley grateful for the help
The result of the 3-way interaction is not significant, which is fine! However the 2-way interactions are very interesting. But our statistician tells me that unless I remove the 3-way the 2-way interactions are not interpretable
I was also suggested to check this by the following - PLEASE COULD YOU TELL ME IF MY CODE IS CORRECT :
Recode one the
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prerona
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AFNI Message Board
Hi
I have an experiment where each subject performs 2 conditions - each having 2 levels. I also have 2 groups. I want to use 3dLME, with age as a covariate.
We want to model for diagnosis (ADHD NT), age + load (3 and 4) and direction (forward and backward).
I ran the code below and I got automatically a 3 way interaction. Using 3dLME can we also omit the 3 way interaction (diagnosis X
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prerona
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AFNI Message Board
We want to control for mean activity within subject across conditions - making both slope and intercept random. Thus we tried
-ranEff 'Subj'
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prerona
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AFNI Message Board
Hi
can someone help me with my 3dLME issue?
I have an experiment where each subject performs 2 conditions - each having 2 levels. I also have 2 groups. I want to use 3dLME, with age as a covariate. We want to model for diagnosis (ADHD NT), age + load (3 and 4) and direction (forward and backward). We wanted to look at fixed effects of diagnosis, age, load, direction, and their interactions
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prerona
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AFNI Message Board
Postdoctoral Scholar Position Available for Neuroimaging and Behavioral Project on Impulsivity and Development in Decision-Making in Adolescence and Young Adulthood
MIND Institute, Department of Psychiatry and Behavioral Sciences University of California Davis
The Attention, Impulsivity and Regulation (AIR) Program at the UC Davis MIND Institute is recruiting a full or half-time positio
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prerona
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AFNI Message Board
I see. It should have been Diagnosis + Age + Interaction. Thank you!
Sincerely
Prerona
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prerona
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AFNI Message Board
Hi
thank you so much! This worked
But is the meaning the same?
sincerely
Prerona
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prerona
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AFNI Message Board
Hi
I am getting this same error with version AFNI_17.2.16
In my experiment I have 2 groups, 2 within subject factors: Direction and Number, and a covariate Age
I want to see the interaction between group and each of the two within subject factors (ie: group X Direction and group X Number), after covarying for age. However, the effect of age may be different in the two groups
So I hav
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prerona
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AFNI Message Board
Hi
I uploaded the files - did you receive it?
Thank you so much for your time!
Sincerely
Prerona
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prerona
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AFNI Message Board
Thank you! That makes sense.
So that means both my datasets should be in MNI though the header says one is in TLRC
Because I normalised that one to a MNI mask at the end of my preprocessing pipeline.
But one may be the "FSL Flavour" as I downloaded it from FSL, I guess
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prerona
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AFNI Message Board
Thank you! So I guess this will tell the actual space and not just the header (in case of a mismatch between these two)?
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prerona
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AFNI Message Board
Hi
I tried this suggestion:
"To transform from TLRC space to MNI space, use the MNI FSL transformation matrix (mni_fsl2tal.1D) like this.
3dWarp -matvec_out2in mni_fsl2tal.1D -prefix dset_mni dset+tlrc "
but my resulting mask still says TLRC for space when I do 3dinfo -space
these are the commands I used:
$ 3dWarp -matvec_out2in mni_fsl2tal.1D -prefix 3dwarp_e mask_A
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prerona
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AFNI Message Board
Hi
could anyone tell me what is the difference between these two commands:
3dinfo striatum-structural-2mm | grep -i 'template'
and
3dinfo -prefix -av_space striatum-structural-2mm
I found them both as suggestion to check the space of a file / image but I am getting different answers from both!
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prerona
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AFNI Message Board
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