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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
Paul is mostly correct. Where he is wrong is that 3dcalc is programmed not to produce NaN or other illegal outputs. So sqrt() of a negative number will return 0, not the NaN (Not a Number) marker for an illegal value. Similarly, log() of a negative number returns 0. Getting a dataset full of NaN values would be a bad thing, so the program won't do it.
3dcalc is a general purpose voxel
by
Bob Cox
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AFNI Message Board
Of course, the answer is in the source code (in file mri_fwhm.c).
/* nonlinear optimization of parameters */
xpar[0] = apar ; xpar[1] = bpar ; xpar[2] = cpar ;
xbot[0] = 0.006 ; xbot[1] = 0.05*bpar ; xbot[2] = 0.05*cpar ;
xtop[0] = 0.994 ; xtop[1] = 5.55*bpar ; xtop[2] = 5.55*cpar ;
pp = powell_newuoa_constrained( 3 , xpar , NULL , xbot , xtop ,
by
Bob Cox
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AFNI Message Board
1800 participants! What kind of study is that? I never designed or thought of 3dttest++ as working with so many datasets at once. I'm a little surprised it worked.
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Bob Cox
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AFNI Message Board
The errts file is already detrended, so you don't need the -detrend option -- but it won't hurt you, either.
The purpose of 3dFWHMx is to estimate the spatial smoothness of the noise in the time series data, so the residuals (errts) are the best thing to input, since they represent the random noise.
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Bob Cox
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AFNI Message Board
Sorry for not getting back sooner.
The problem with sign randomization on just 6 datasets is that there aren't that many sign combinations. With a total of 16, I can add permutation to the mix, which would make the calculations combinatorially possible. However, I'm literally working on that code today, and have to test it, and then package it up for mass consumption (e.g., write s
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Bob Cox
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AFNI Message Board
I would be hesitant to recommend the use of 3dFWHMx on non-FMRI data -- we have no experience with that, and trying to "hack" around the statistical impositions of SPM (say) by side-tracking through AFNI-land is kind of oogy IMHO.
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Bob Cox
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AFNI Message Board
It is possible to use -stim_files with 0/1 files correctly, but it is not easy. It is better to use make_stim_times.py to convert the 0/1 files to timing files.
If you want a fixed shape HRF, then 'BLOCK(d,1)' is a good starting choice, where the number d is replaced by the duration of the stimulus (in seconds).
If you want a variable shape HRF (also known as a FIR model), you ca
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Bob Cox
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AFNI Message Board
The "usual" way to use 3dDeconvolve is to provide a timing file that gives the start times for each stimulus (which are not required to be on the TR timing grid) -- this file is specified using the -stim_times option.
For the HRF, you choose a model function to define the shape of the response for the stimulus. There are many options for that.
The "best" way to run 3dD
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Bob Cox
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AFNI Message Board
You have figured it out! Except for a couple of details:
(1) You want to start with 10 to skip the first 10 time points
(2) Since the output 1D files are columns (each row is one time point), you want to select a subset of rows, which would be done using the subscripts '{10..$}' -- here, $ means the last row and the curly braces {.} are used for row subset selection -- the squar
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Bob Cox
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AFNI Message Board
At this time, 3dNwarpCat cannot save the results from multiple line matrix concatenations with a nonlinear warp -- because the result would be multiple nonlinear warps, and I don't have a file format for that (and the multiple warp file could be gigantic in size).
Only 3dNwarpApply can do the multiple line matrix concatenations, and it does these "on the fly", so only one catena
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Bob Cox
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AFNI Message Board
Do you see individual subject "activations" that make sense? In a lot of subjects? In overlapping places?
If the answers are "yes, yes, yes", (or even "maybe, maybe, maybe") then a little more blur -- 6 or 8 mm -- might help. An additional possibility is to re-run the individual subject analyses with the addition of AnatICOR de-noising and nonlinear anatomical
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Bob Cox
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AFNI Message Board
This message was added a few months ago, so if you updated your AFNI recently, you could start getting the message even in situations where it did not appear before -- because it wasn't in the program before.
Do you see results that make sense? The warning says that in any individual voxel, the strength of the statistics is weak. This does not mean there are no true multi-voxel (cluster
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Bob Cox
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AFNI Message Board
Certainly the ACF parameters should be estimated from the whole brain residuals -- it is very not a good idea to estimate them from a small region.
Otherwise the normal caveat about small volume correction are still present -- were the ROIs selected via some unbiased reasoning?
Another option to consider, if it applies to your situation, is the new 3dttest++ -Clustsim option, with the appro
by
Bob Cox
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AFNI Message Board
Obviously, I've seen this before, which is why I programmed in the re-connection attempt.
What you are seeing is 2 different types of inter-process communication. First you get the messages
Opening NIML socket 'tcp:localhost:53213' to AFNI. Connected!
++ NIML connection opened from 127.0.0.1 (tcp:host:53213,AFNI_GroupInCorr_NIML)
The first one is from 3dGIC, saying it
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Bob Cox
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AFNI Message Board
Well, the first suspect is the labels in the covariates file. What does it look like?
by
Bob Cox
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AFNI Message Board
You aren't giving enough information to tell what kind of system you are using!
What is the output of the command afni --ver ?
Or the command afni_system_check.py -check_all ?
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Bob Cox
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AFNI Message Board
As Rick says, our estimation of smoothness of the noise is based directly on the noise (the residuals themselves), not on some summary statistics of the noise. I've never thought about how to estimate smoothness from the mean square of the residuals.
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Bob Cox
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AFNI Message Board
Yes, but all the problems of limited time points still apply -- if you have only 70 good time points, and bandpass out a large frequency range, you may have very few effective data points left. There is no solution (that I know of) for that kind of problem.
3dTproject does allow for censoring as it bandpasses, unlike the other programs. Read the output of 3dTproject -help for details.
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Bob Cox
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AFNI Message Board
Well, the button-click method works on my system. What system are you running on? What is the output of the command afni --ver?
You can also start the plugin from the Datamode->Plugins menu.
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Bob Cox
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AFNI Message Board
We now recommend you use 3dTproject, which can do other things besides bandpassing at the same time,
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Bob Cox
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AFNI Message Board
The workaround is to set environment variable DYLD_LIBRARY_PATH to be /opt/X11/lib/flat_namespace
This is best done in the login script for your shell. If you use tcsh (as I do), that file is .cshrc in your home directory, and you would add the command
setenv DYLD_LIBRARY_PATH /opt/X11/lib/flat_namespace
to that file. By itself, this will have no effect -- until you start a new shell (comm
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Bob Cox
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AFNI Message Board
Well, I have this problem on my laptop also, and can't get XQuartz to work with AFNI at all, no matter what version I install. I'm going to update my OS and reinstall everything this weekend -- partly because the NIH insists that I upgrade my version of Mac OS X for security reasons.
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Bob Cox
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AFNI Message Board
I'm not sure what your question is. If you are interested in how censoring affects your results, try it! That is, take some data that doesn't require much censoring, and add some censoring randomly to see how it changes. I have not developed any theory to account for this effect, nor do I plan to.
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Bob Cox
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AFNI Message Board
Everyone please note!
A WARNING message is not an ERROR -- it is something that you should be aware of, and evaluate in the context of your particular data analysis.
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Bob Cox
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AFNI Message Board
I'm sure Rick will chime in, but the AFNI point of view is that all the regression and filtering should be done in one step, not in two steps. That is what the 3dTproject program is for -- it will "project out" (the mathematical lingo) the nuisance regressor, including the cosines and sines for the frequencies being rejected.
Rick's super-script, afni_proc.py, can do all o
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Bob Cox
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AFNI Message Board
No, there's no interactive way to do that. However, you could use InstaCalc inside AFNI to avoid having to create a temporary dataset with 3dcalc.
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Bob Cox
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AFNI Message Board
3dClustSim does not actually read data files (at least, the way you are using it) -- the program just creates simulated data in memory and processes it. So it can use the CPUs at nearly 100%. In the jargon of computing science, it is "compute bound".
3dFWHMx, on the other hand, does pretty simple calculations after reading the dataset in (the -acf computations are a little more com
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Bob Cox
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AFNI Message Board
3dDeconvolve was not retro-fitted to allow for voxel-wise regressors. That program is old and spaghetti-code-like, and I deemed it too hard to patch it up. That is why I only added voxel-wise regressor capability to 3dREMLfit. If you really want OLSQ results with Anaticor, you can get those by adding the appropriate '-Obuck' option to the 3dREMLfit command.
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Bob Cox
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AFNI Message Board
AFNI does not use Gaussian Random Field Theory, unlike SPM and FSL.
by
Bob Cox
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AFNI Message Board