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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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The results image is of a seed ROI-based correlation with the rest of the brain WITHIN one condition's betaseries estimates (strong beat). I get equally widespread correlations for our other ROI seeds as well.
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daanderson
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AFNI Message Board
Re-opening this topic because I have run into same high correlation issues mentioned previously (New results image at bottom). Note: We have swapped over to the recommended Beta-series estimation approach (Thanks Gang for patience and recommendations there). Now looking for assistance trying to sort out where these excessively high correlations are still coming from. Included below are scripts th
by
daanderson
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AFNI Message Board
Very helpful Gang. I hope you can bear with a few clarification questions ~Dane
> help file for 3dfim+ appears to say its old and not being maintained. Is 3dDeconvolve now the preferred approach these days?
>>Even though 3dfim+ will not be updated, it can still be used as long as you adopt the same or similar model formulations. In fact, you can directly obtain the output for cor
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daanderson
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AFNI Message Board
Hi Folks,
Loosely following Andrew Jahn's BetaSeries tutorial https://www.andysbrainblog.com/andysbrainblog/2014/05/creating-beta-series-correlation-maps.html and he has 3dfim+ for the seed/ideal to whole brain correlation step. However help file for 3dfim+ appears to say its old and not being maintained. Is 3dDeconvolve now the preferred approach these days?
If so:
A. What is pro
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daanderson
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AFNI Message Board
Thank you Dr. Gang (as always). I will have to do some more reading on beta series to get my head around the approach.
One thought our team had in response to your concerns was running Seed-to-whole brain FC correlations analysis using only non-overlapping/interleaved portions of our condition of interest for the seed signal to avoid the modeling/deconvolution issue. Would there be any concept
by
daanderson
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AFNI Message Board
Definitely appreciate the candor. Have a few follow up questions:
- Can you explain a bit more about what is the root of difficulty is for untangling the condition's task-based signals? Is it experimental design (rapid interleaved), limited modeling capability (simple block and HDR), amount of data, etc.?
- Could beta series analysis output coefficients be used to estimate a timeser
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daanderson
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AFNI Message Board
Hi Dr. Chen,
We spoke about the experimental design and 3dSynthesize a bit in a previous posting: https://afni.nimh.nih.gov/afni/community/board/read.php?1,162913,163126#msg-163126 Let me know if you have questions after reviewing.
You did raise the option of beta series to measure trial by trial correlations there. Definitely see the advantage however the end goal is to do some effectiv
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daanderson
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AFNI Message Board
@ PTaylor - Yes we do have full Fstat, R, T, V, and GLM condition comparison analyses. Not sure which additional output would be of assistance with the FC analysis but please let me know.
For more context: The activation analysis was originally done years and years ago before afni.proc was the primary approach. Specifically we used 3dDeconvolve with DmBlock and AM times (See below). Now we ar
by
daanderson
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AFNI Message Board
Really great avenue to attack. Definitely improved things but let me address points in order:
1. We are using motion correcting and censoring at 0.3. These seemed quite effective at the activation stage and same parameters are being used now in FC
2. For 1D file we removed motion and censors via "select -Baseline" and "cenfill none' in 3dsynth/3dcalc stage of creating our
by
daanderson
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AFNI Message Board
Hi AFNI folks,
Hoping for some guidance on 2 things:
1. In running some task based ROI-to-Wholebrain results through the simple Correlation approach outlined by Gang's old webpage (3dDeconvolve > R^2 > R > Z > 3dTtest++), I ended up with very very high internal correlations (see first attached image). What is the proper approach to correct for the massive multiple compariso
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daanderson
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AFNI Message Board
Sincerely appreciate the information Mr. Glen. Unfortunately as seen in attached both Brainnetomme and Glasser have the same problem with the STG areas completely outside the N27 brain (as seen below). This brings a few questions to help me plot a way forward:
1. Does utilizing MNI atlases for ROI really require registering all functionals to an MNI 2009c anatomical then?
1b. What is
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daanderson
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AFNI Message Board
Hi Mr, Glen,
Per your comment regarding TT Daemon not aligning well with TT_27, I have certainly noticed this (See first image). However when extracting similar regions from the Brodmann_MM atlas recommended in this old thread I am finding same issue with BA22 having sections WAY outside the brain (see second image).
Is this to be expected, ie. always an issue of TT vs MNI atlas alignment
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daanderson
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AFNI Message Board
Thank you gents, one and all. Updated binaries and things worked as expected. Much appreciated.
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daanderson
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AFNI Message Board
Appreciate the help Mr. Glen. Unfortunately I only seem to be able to get the following warnings, even when varying <>, "", [], area name/code, and X values I only seem to be able to get the following:
- output sub-brick 0 is all zeros!
- Symbol x using predefined value
- can't open dataset /Users/Credo/abin/TT_caez_mpm_22+tlrc.Area_TE_1.1
I am comfortable splitting
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daanderson
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AFNI Message Board
Hi AFNI folks,
Please see attached screen grab of my struggles. Trying to export the TE 1.1 area from the CA_22_MPM atlas but for some reason it wont recognize the area name or the area code unlike TE 1.0 and 1.2. Tried dozens of variations. Is there something obvious I am missing here?
Alternative question: Anyone know of an atlas that has a well accepted Primary Auditory Cortex region p
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daanderson
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AFNI Message Board
Appreciate patience with response. Will try to touch on each topic below:
~Dane
Duration modulation: The auditory stimuli (both "Strong" & "Weak") involved the same number of identical tones which varied only in their patterns and inter beat intervals (IBI - 100s of Milliseconds between tone onsets). Practically speaking these differences meant the stimuli duration
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daanderson
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AFNI Message Board
Thank you for swinging back around, and especially patience/perspective with the follow up questions below.
~Dane
Regarding dmUBlock: My understanding was that this was a variant used for PPI analyses where you had a psychological measure/performance value that varied and could be applied as a potential moderating factor. Unfortunately while our task actually has "strong" vs. &qu
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daanderson
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AFNI Message Board
Hi AFNI wizards,
I am returning to an old dataset I previously undertook an activation analysis on to run some ROI-to-ROI FC network analyses and have a few questions (further task context below if needed):
1a. How does 3dDeconvolve determine the duration(#of TRs) of its modeled HDR function from an stim-times_AM(1) 'dmBLOCK(1)' set of stim-times in the output .xmat stimulus colu
by
daanderson
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AFNI Message Board