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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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We do not know if the continuous independent variable (chocolate loving on the Godiva scale) changes between the two preferences.
That's what we want to find out via AFNI/imaging.
Put in more realistic terms, we have kids from across the range of irritability--with ratings of irritability on a continuous scale.
This is not a standard dichotomous group AFNI analysis.
Meaning--th
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Ddickstein
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AFNI Message Board
My hypothesis is the greater levels of chocolate love on the Godiva scale are associated with increased striatal activity during a food preference task when picking desserts vs. asparagus.
I thought it would be interesting to keep the independent variable continuous/scalar (score on Godiva scale of chocolate love).
But--maybe that's not possible within AFNI?
And I have to go the sta
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Ddickstein
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AFNI Message Board
Task types/events--several.
Was trying to go "full RDoC"-and keep the sample dimensional/continuous--without dichotomous/bifurcated/categorical groups.
Is that possible?
If not--then--I guess--I have to define cut points--for a standard analysis (high vs low chocolate love--rather than full dimensional).
Tnx Gang and hope you're ok!
-Dan
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Ddickstein
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AFNI Message Board
Yes--I want to know the effect of the quantitative/continuous variable.
To see if the higher your chocolate-love score, the greater your accumbens area activation is when making a decision.
(example is embellished to make the point--not really doing a study of chocolate love)
-Dan
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Ddickstein
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AFNI Message Board
What's the best way to use a continuous independent variable to analyze task-based fMRI data within AFNI?
ie IV=continuous 1-10 scale of how much you like chocolate to analyze DV=neural activity during a decision-making task?
(In contrast to the usual dichotomous IV between-group choco-lovers vs choco-haters).
Tnx!
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Ddickstein
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AFNI Message Board
Re-reading your reply from April--and suggestion to use 3dQwarp rather than SSwarper. Having read the help for that program, and postings on the afni board--questions: (1) how do we know that my university's SLURM server is running the correct updated version of 3dQwarp--as it looks like there are frequent changes to that program? (2) do you have an example of typical 3dQwarp usage that wo
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Ddickstein
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AFNI Message Board
Can you point me in the direction of where your team has answered what I think must be a common question:
how do you handle registration/normalization if someone gets out of the scanner and then back in?
Meaning--subject does structural scan and 3 runs of fMRI task; has to get out to use bathroom; gets back in to finish other 3 runs and we do a 2nd structural scan just to have it.
When
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Ddickstein
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AFNI Message Board
Tnx for speedy helpful reply!
To confirm--I first have to run the SS Warper command--which itself takes a while.
And then--run the script I sent for the AFNI_PROC.py part (which will also take a while but faster on cluster running multiple threads?
(vs my MacBook test of 1 subj x 12 hours at sub brick 134 on 3dLocalstat).
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Ddickstein
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AFNI Message Board
Was playing around with resting state data using new to me tools of SS Warper combined with Afni_proc.py with anaticor (akin to example 9B but with B-O-B's SS Warper suggestions).
Questions:
(a) is this a reasonable combination of SS Warper results with AFNI_PROC?
(b) any suggestions for speeding this up?
Was playing on my quad core MacBook Pro to test it before rolling it out
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Ddickstein
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AFNI Message Board
Thanks Daniel for your response! Realizing the limitations of the Talairach atlas, and everyone's time--is there a way to fix this/nudge them so they would be correct? At least the BA ones on edge of cortex that need a slight nudge to be on brain? As for AFNI folks in the universe, this not only would help ROI analyses, but it affects interpretation of the awesome WHEREAMI function. Thanks
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Ddickstein
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AFNI Message Board
I used the draw dataset plugin to make an anatomical BA 47 mask from the TT_N27+tlrc template. But--when I render it as overlay--it is off--more lateral and somewhat superior to actual TT_N27 anatomical. If I click "where am I" on the part that is lateral/not on top of anatomical--afni says I'm smack on BA 47. Any ideas--as I do not want to mis-apply a mask to my analyses. Than
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Ddickstein
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AFNI Message Board
If anyone is out there in AFNI-land, given government craziness--I'm having trouble with the afni gui/interface. Specifically--clicking on buttons like clusterize or set p-value, is acting weirdly. Clusterize button won't click or open settings so I can use it. P value setting opens dialogue box--too small--that if I stretch--I can not enter a number or any text. Yesterday--I had to
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Ddickstein
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AFNI Message Board
What does this warning mean--as part of afni_proc.py script: "WARNING: Input dataset is not 3D+time; assuming TR=1.0"
Pasting bigger chunk of output: ++ 3dTstat: AFNI version=AFNI_17.2.02 (Jul 10 2017) [64-bit]
++ Authored by: KR Hammett & RW Cox
*+ WARNING: Input dataset is not 3D+time; assuming TR=1.0
echo average errts FWHM blurs: 8.82189 8.99374 8.18736 8.66061
averag
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Ddickstein
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AFNI Message Board
Tnx, Rick!!
I used 3dinfo.
What you said is there...including fact that inputs were dcmS000XAXXXXIXXXX etc (Siemens tim trio).
But none of info that we input at scanner (DOB, Sex, Weight).
Thanks--and Happy Holidays to you an all AFNI staff (and AFNI Users)!!
-Dan
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Ddickstein
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AFNI Message Board
If using to3d to convert Siemens dcm files to afni brik/heads, will any identifying info entered at scan (date of birth, age, sex) be left in the residual afni brik/heads?
If yes, is there an afni program to remove this info?
Tnx, and happy holidays!
-Dan
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Ddickstein
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AFNI Message Board