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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
I don't know. You could ask the creator of the atlas. Here is his academic web page:
by
Bob Cox
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AFNI Message Board
Links to the article pre-prints on the arXiv:
Summary of the BC paper [1 page] -- https://drive.google.com/open?id=0B6Sn11ZTBrhvR2VYWmhvYmpZU2M
Brain Connectivity -- https://arxiv.org/abs/1702.04845
PNAS -- https://arxiv.org/abs/1702.04846
And the slides -- https://drive.google.com/open?id=0B6Sn11ZTBrhvMi1TRDdKRUlMaEk
by
Bob Cox
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AFNI Message Board
During the past year, the topic of clustering and false positives rates in FMRI group analysis has been widely discussed both in research circles and in the popular press. A number of very strong claims were made in the initial paper by Eklund et al (2016, PNAS), both about previous methods in general and about AFNI in specific.
These are all important issues for our group. We have addressed
by
Bob Cox
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AFNI Message Board
Yes. The simplest way is to leave the "Pos" button at the bottom of the colorscale UN-checked, and then do this:
a) right click on the label at the top of the threshold slider to get a popup menu
b) about 2/3 of the way down is a chooser labeled "Sign"
c) by default, this chooser is set to "Pos & Neg"
d) change it to "Neg only" to see only voxels
by
Bob Cox
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AFNI Message Board
The problem has been solved. It had to do with differences in the implementation of thresholding in the clustering code and in the main AFNI GUI. The fix is explained below, in an excerpt from README.environment (as I edited it yesterday). However, you'll have to wait until we re-compile the binaries. I hope to remember to do that tonight, but my aging brain doesn't remember things
by
Bob Cox
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AFNI Message Board
I've got the corrected data and am looking at it now.
I think what you are seeing is due to the intersection of 2 functions in AFNI.
The overlay is at a lower resolution than the underlay, so it is resampled to match to underlay grid for display. The default resampling method is Linear interpolation.
Your overlay data isn't some value that is more-or-less continuous in space (suc
by
Bob Cox
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AFNI Message Board
The only file uploaded by you that I see has only the files
README.txt
conj_SVcho_ep+tlrc.BRIK
conj_SVcho_ep+tlrc.HEAD
The latter two look like a dataset, but the HEAD file is a copy of the BRIK file and so useless. I have deleted the upload with your name on it. Can you check to make sure the HEAD file has a different file size than the BRIK file, and that 3dinfo works when run on the
by
Bob Cox
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AFNI Message Board
At this point, I can only suggest packaging up the files (underlay and overlay) that aren't working nicely together, and sending them to us. This link should work for that purpose.
by
Bob Cox
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AFNI Message Board
(1) I no longer recommend the use of the -fwhm or -fwhmxyz options. Instead, I recommend that you use 3dFWHMx -acf to get the mixed Gaussian+exponential model fit parameters (a,b,c) from your subject level residuals, take the mean of those across subjects, and use those as input to 3dClustSim with the -acf option. If you are using an up-to-date version of afni_proc.py for your individual subject
by
Bob Cox
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AFNI Message Board
First thought -- check the Alpha setting for functional overlays. This is the variable
AFNI_FUNC_ALPHA which is set in your ~/.afnirc file (or perhaps in your shell login file).
You can check this setting inside AFNI -- where it counts -- by looking at the color overlay "pbar" underneath the OLay label at the top of the Define Overlay control panel. If that pbar shades left-to-rig
by
Bob Cox
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AFNI Message Board
Gang -- didn't you get TENTzero and TENT exactly reversed in the previous post!?
by
Bob Cox
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AFNI Message Board
You don't give enough information to even begin to think about the problem! This does not happen here, so there must be something peculiar about your system.
What is the crash message? What is the output of the command below?
afni_system_check.py -check_all
by
Bob Cox
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AFNI Message Board
I still don't understand what you mean by "mask" in this context. How is "M vs. baseline" a mask?
by
Bob Cox
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AFNI Message Board
What do you mean by "mask the response" in this context? Do you mean modulate? Or mean to compute the amplitude of M and 1/2/3 separately, even if they are close in time?
by
Bob Cox
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AFNI Message Board
As rick suggests, add the option -volreg_warp_dxyz 2.0 to your afni_proc.py command and try again.
by
Bob Cox
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AFNI Message Board
3dvolreg estimates the amount of movement. But since image registration is not perfect, it's not possible to take an MR image (3D volume) with a large amount of movement and make it look the same as if the subject had never moved.
So afni_proc.py will cast out (censor) volumes (time points) when there was too much movement relative to the previous volume.
By default, we have set this
by
Bob Cox
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AFNI Message Board
Teaching AFNI here at Wash U (St Louis), we've seen a few people with a peculiar problem: they can't type into AFNI popup windows, such as "Jumpto xyz".
The solution to this difficulty is to set an environment variable:
setenv DYLD_LIBRARY_PATH /opt/X11/lib/flat_namespace
which applies when you are using a new version of the XQuartz server program. I've not seen
by
Bob Cox
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AFNI Message Board
The choice between the 3dMVM and 3dttest++ programs depends on the statistical model you have for the signal inside your data. Rather than try to explain those points of the program here, I'll point you to the group analysis presentations from which we teach. Follow the link below and get the afni24 and afni25 PDFs.
https://afni.nimh.nih.gov/pub/dist/edu/latest/afni_handouts/
by
Bob Cox
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AFNI Message Board
And in general, I think it is a bad idea for someone who does their entire analysis, including group statistics, in FSL or SPM or any other package, to turn to 3dClustSim to validate their results.
In the near future, I am going to disable the Gaussian spatial autocorrelation function (ACF) option in our clustering software, and only allow the use of the more complex "mixed" ACF mode
by
Bob Cox
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AFNI Message Board
The problem comes from the fact the that output dataset is created in memory and only written to disk at the end. So if the output dataset gets HUGE, then you run out of memory (which is usually what "killed" means).
To get around this, you could do (as you suggest) a separate 3dNwarpApply for each TR. However, that would be slow, with a lot of file I/O.
You could do a bunch of
by
Bob Cox
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AFNI Message Board
I would recommend you start with doing just head motion correction. The effect of head movements on FMRI data can be huge, and so removing them (as much as possible) is important. In particular, since the head moves as a unit, head motion produces highly correlated signal changes across wide regions of the brain. In FMRI processing, it is common also to linearly regress the 6 estimated movemen
by
Bob Cox
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AFNI Message Board
Your questions are too vague to answer, and you don't give enough information about your planned analyses to provide any advice.
What do you mean by "voxel-wise analyses"? That's pretty much all that the standard AFNI programs do, and they do the preprocessing steps that you mention. Where did you hear "that in voxel-wise processing some of these preprocessing should
by
Bob Cox
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AFNI Message Board
Your question may sound simple, but it is not -- at least, the answer is not simple.
3dClustSim is based on simulating the noise field that interferes with detection of the "true" signal in the dataset. To do this simulation, the program needs some statistics about the the spatial smoothness of the noise. For the case of FMRI time series analyses, these statistics come from analyzi
by
Bob Cox
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AFNI Message Board
The absence of the "Set p-value" popup is secular. I am also using XQuartz 2.7.11 on my Mac laptop and I get that popup. Do other popups go missing as well (like the Underlay chooser, or the "Set q-value" chooser)?
Try minimizing the AFNI controller window (to the Dock), then bring it back. Does that help? I'm really just guessing here, since your problem doesn
by
Bob Cox
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AFNI Message Board
Check which version of XQuartz you are running (from the "About XQuartz" menu item on the Mac menu bar item for "XQuartz"). Here's a message from AFNI that might be relevant (or might not be):
++ If you are using XQuartz 2.7.10 (or later), and
+ AFNI crashes when opening windows, you might need
+ to set an environment variable to solve this problem:
+ setenv D
by
Bob Cox
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AFNI Message Board
What you ask is not unreasonable, but it is not something I've considered doing. It would take some effort, since that old program was not written with parallelization in mind, so make it work with multi-threading would require a careful examination of the code. Without a stronger argument than you give, it's not worth my effort.
by
Bob Cox
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AFNI Message Board
Here is a script I have used recently to analyze a lot (198) of datasets. This script was used to warp the Cambridge subset of the FCON-1000 collection. It uses auto_warp.py, since that makes it easy to use the warped results with afni_proc.py in turn. The script below takes on the command line one argument, the subject ID; e.g, the command
tcsh warper.csh sub00156
will work on dataset anat_
by
Bob Cox
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AFNI Message Board
You can use the ccalc program to try out AFNI expressions. As in
calc> sqrt(-1)
Z = 1
calc> log(-3)
Z = 1.09861
calc> log(3)
Z = 1.09861
calc> log(0)
Z = 0
Showing that I was wrong in my previous post: sqrt(x) is really sqrt(abs(x)) (similarly for log()). Note log(0)=0, an indication of avoiding blowups.
The calc programs are based on some functions I wrote in the mid 1
by
Bob Cox
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AFNI Message Board