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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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Can you clarify your reply to the second point? A missing word perhaps. Did it need to read 'are controlled with age'?
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swijeakumar
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AFNI Message Board
Hi Gang,
Thanks for clarifications. That worked. I see that running this model gives me main effect of Load, chrom, AgeD and interactions between the three. This looks like what I want to move forward. I want to clarify further on the interpretation of the clusters of activation for effects that show an interactions with AgeD versus no interactions with AgeD.
Does this sound correct:
In an i
by
swijeakumar
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AFNI Message Board
This was a hypothetical question. I ran the two models after I wrote this and actually checked the effects in the bucket across the two. Apparently, the results are identical i.e. no differences in the clusters between Models A and B. Is this expected?
Sorry to bombard your feed. I inserted some GLTs into my 3dMVM model but running this script gives me an error message saying ' Failed at
by
swijeakumar
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AFNI Message Board
Hi Gang,
Sorry to bombard your feed. I inserted some GLTs into my 3dMVM model but running this script gives me an error message saying ' Failed at GLT No. 7! Make sure that the model or GLT specification syntax is correct'
It seems to have a problem with my covariate line. I tried different placements. Any advice?
3dMVM -prefix /Volumes/DRIVE4/Shivgarh_data/GroupResult/VWM/Both
by
swijeakumar
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AFNI Message Board
Hi Gang,
Thanks for this. Yes, this makes sense. To complete my understanding, one more follow-up:
Let's say Model A had AgeD as a covariate and Model B did not.To be clear, both models still have load and chrom as within subject factors.
Here, would you say that a cluster of activation that showed up as a load main effect for Model B but not Model A was one where activation varied as
by
swijeakumar
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AFNI Message Board
Thanks for this Gang, just a clarification and follow-up of point 3:
Would it be possible to look at the interactions between AgeD and load and/or chrom ( as a whole) instead of (or perhaps, in addition to) the effects of AgeD on each of the levels of the factors (as you have shown in point 2)? But, maybe this is what you mean in point 1, when you say the effects in the bucket are controlled f
by
swijeakumar
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AFNI Message Board
Hi Gang,
Thanks for clearing out my questions with co-variates for 3dMVM. I have a couple more questions. I have also copied by script below for reference.
1. Do the outputs of load main effect, chrom main effect and interaction between load and chrom after the effect of AgeD has been estimated or is this without the effect of AgeD? It doesn't indicate so when I pull up each of these F
by
swijeakumar
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AFNI Message Board
Each kid has a value for each of the three levels of load and each of the two levels of chromophore. So age wouldn't vary between load 1, load 2 or load 3. Similarly, age wouldn't vary between chromophore 1 and chromophore 2.
As an e.g..:
Age(days) Load Chromophore Inputfile
1000 1 1 xyz1.nii
1000 1
by
swijeakumar
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AFNI Message Board
Hello there,
I have a question about 3dMVM and covariates
My 3dMVM analysis has two within subjects factors - load (3 levels )and chromophore (2 levels). These are data from infants and children of different ages, but each infant/child has a value for each level of a factor. We think that our effects be it main effect of load and/or main effect of chromophore and/or interaction between load
by
swijeakumar
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AFNI Message Board
Sorry, I'll start over just to make sure everything is clear.
I have 20 participants. Ten of them did Task 1 on Day 1 and Task 2 on Day 2. The other ten did Task 2 on Day 1 and Task 1 on Day 2. We collected resting state scans before and after each Task. I'll refer to them as pre-Task1 scan, pre-Task2 scan, post-Task1 scan and post-Task2 scan (This is 'Time' factor).
I
by
swijeakumar
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AFNI Message Board
Hi Gang
Sorry to dig this up again, but I just wanted to follow up on another issue on this post. Here's is the info from my first post for reference:
So I have the following dataset:
Set A of ten subjects did Task 1 on day 1 - pre-task resting state and post task resting state
Set B of ten subjects did Task 2 on day 1 - pre-task resting state and post task resting state
Set A
by
swijeakumar
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AFNI Message Board
Hi all
I would appreciate any input on the issue I raised above.
Thanks!
S
by
swijeakumar
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AFNI Message Board
Hi all
I have a basic design efficiency question.
I want to report the efficiency of two model designs using 3dDeconvolve.
What metrics do I use to compare the models? Do I use the signal +baseline condition number (higher the better) and the matrix inverse average error (the lower the better)? Interestingly, both my models have similar numbers for these metrics but one of them (predict
by
swijeakumar
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AFNI Message Board
Hello there
I'm not sure this is a even a possibility but thought I would ask anyway. Is there a way to plot the drift-corrected time series from regressing just the polynomial drift (polort) after using a 3dDeconvolve? Is there a flag I could use to extract this put or a file that 3dDeconvolve spits out in the process?
Thank you for any advice.
Sobana
by
swijeakumar
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AFNI Message Board
Hi all
I have a question about using whereami function in terminal versus the whereami option in the GUI. As I understand it from a previous post that if you enter -dset flag in the whereami function, it will use the template space of the input data test and display information in that space as well as transform it to the other spaces too. Is this accurate?
Now, if I were to pull up the fil
by
swijeakumar
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AFNI Message Board
Sorry, I forgot to add..
The input correlation maps are z transformed correlation maps.
by
swijeakumar
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AFNI Message Board
Hi all
I noticed there are a few updates with 3dClustSim and I wondered what the best way to use it for an ANOVA main and interactions maps created from a group analysis of resting state datasets was. For eg.
Should I use a a file with bucket sub-bricks of resting state maps for a network from all my subject (eg. File dmn.nii.gz has 20 sub-bricks for 20 subjects) and estimate the smoothness
by
swijeakumar
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AFNI Message Board
Thanks. Turns out I had to install El Capitan anyway and after that when I tried to re-install afni and update, it worked. So all good. Thanks.
by
swijeakumar
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AFNI Message Board
Hi Daniel
This is the update that I mentioned seeing (in the first post of mine). I downloaded the script and tried to run it but it said command not found.
Any advice?
S
by
swijeakumar
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AFNI Message Board
Hi there
I tried to update afni on both my macs and I seem to be getting this error. I saw an update this month but I can't seem to get the script to run either. Any advice would be appreciated.
bash-3.2$ @update.afni.binaries -defaults
-- have AFNI binaries under /Users/sobanawartinywijeakumar/abin
-- install dir: using existing /Users/sobanawartinywijeakumar/abin
-- attempting t
by
swijeakumar
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AFNI Message Board
Thanks for your reply. I should clarify. this is what I meant:
I have a total of 20 subjects worth of data.
10 of 20 subjects did Task 1 on Day 1 and Task 2 on Day 2 - pre-task resting state and post task resting state
the other 10 of 20 subjects did Task 2 on Day 1 and Task 1 on Day 2 - pre-task resting state and post task resting state
So this still leaves me with the same issue, co
by
swijeakumar
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AFNI Message Board
3dMVM - 8 years ago
Hi all
I have a stats cum 3dMVM question. So I have the following dataset:
Set A of ten subjects did Task 1 on day 1 - pre-task resting state and post task resting state
Set B of ten subjects did Task 2 on day 1 - pre-task resting state and post task resting state
Set A of ten subjects did Task 2 on day 2 - pre-task resting state and post task resting state
Set B of ten subjects did Task
by
swijeakumar
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AFNI Message Board
Hi there
I had a query about scaling the beta coefficients to percent signal change which then lead to checking my script to make sure I have all the nuts and bolts for any fMRI analysis. I have attached parts of the script I use. Can you clarify on the stance of normalisation when one stitches together multiple runs? what is best way to scale or normalise? Is it better to run the analysis and
by
swijeakumar
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AFNI Message Board
I see. So if the data set that I want to run whereami on is in MNI space, then I should specificy -space option to be MNI and consequently, report the MNI coordinates from the wherami's output. Is this correct?
by
swijeakumar
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AFNI Message Board
Hi all
Quick question on the whereami function.
If my datasets are in a specific space, is it the case that I should be using only the coordinates reported in that specific space or can I use TLRC or MNI, because the whereami function does the spatial transformations and has reported the coordinates accordingly in all the spaces?
On a relevant note, if my images are in MNI space and i
by
swijeakumar
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AFNI Message Board
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