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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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Pages: 12345
Results 61 - 90 of 144
At this point, I (the author of 3dttest++) am a little confused.
Rather than kibitz your problem, I'll need to look at it.
For that purpose, I'll need access to your data and the commands used to run the analyses.
Either you can put it on a place where I can get at it (e.g., DropBox), or you can upload it to our server -- I believe the correct address for that is still
Please
by
RWCox
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AFNI Message Board
Well, I'm not sure what your goal is, but you can orthogonalize a set of vectors using the 1dsvd program with the -1Dleft option. However, I'm not sure that will move you in the direction you want, but I can't really tell what your goal is.
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RWCox
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AFNI Message Board
Hmmm. I just tried a similar command on my system and it worked.
I just now made some changes to the way NIFTI filenames are processed/stored inside the dataset structure. This will change the way the filename appear in messages like you got, but shouldn't affect the operation in any other way. (I replace the filename given on the command line with its "realpath" - the actual fi
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RWCox
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AFNI Message Board
"Experimental" in AFNI-help-speak means that the program has not be used in a lot of cases. Which describes 3dLocalACF - as far as I know, I am the only person who has ever run this program. Any changes will only come when the program gets used again (by myself or by YOU), and issues arise.
The lower limit of at least 39 time points is from the fact that the first thing computed by t
by
RWCox
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AFNI Message Board
There are a few of the statistics that 3dTstat computes that depend on knowing the correct TR. But only a very few. For the vast majority, including what you have given as an example, knowing the TR is not needed. But the program puts out the WARNING just in case, since it isn't clever enough to decide when the message is actually needed.
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RWCox
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AFNI Message Board
There is a reason that blurring to a given FWHM is not allowed inside small masks. Estimating the FWHM accurately requires a decent number of voxels, and blurring to FWHM requires doing that estimate over and over as the blurring magnitude is increased.
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RWCox
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AFNI Message Board
Hola Stefano,
The statistics computed in 3dDeconvolve are between a "signal" model and the "non signal" model (S and N in what I write below).
What regressors are considered to be in S and what are considered to be in N depends on the statistic being computed.
The statistic bricks measure how much adding S to N improved the least squares fit.
For individual regressors
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RWCox
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AFNI Message Board
You might experiment with pre-processing your subjects' T2 datasets with 3dUnifize and its '-T2' option.
Also, you can (with the default weighting) use the '-wball' option to add more weight to the region you like the most. My limited experiments on this, focusing on the thalamus, used '-wball 0 14 6 30 40' where '0 14 6' are the xyz coordinates of
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RWCox
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AFNI Message Board
The logic of 3dAutomask with a clip level of 0.33 is used to form the base image automask, after the base image is smoothed a little (4.5 voxels FWHM). Then the voxels surviving inside the automask are scaled to make the weight. This is the only function of the automask. The alignment proceeds with the weight volume which is separate from the base image volume. That volume is usually blurred a li
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RWCox
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AFNI Message Board
I just uploaded changes to the GUI to allow locking of zooming and panning (but not cropping) between windows from different AFNI controllers. That is, when 'Zoom lock' is enabled, axial image viewers from different controllers with zoom and pan together.
It's kind of fun, actually. This feature will be available in stores for Christmas. And on our website for Hanukkah. Maybe ev
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RWCox
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AFNI Message Board
I suppose Zoom and Crop/Pan could be locked, but cannot be at this time.
I'd have to look into the code to see how to do these.
Zoom would be pretty easy, as I recall the way it's implemented, and it's a straightforward thing with only 4 discrete choices (1, 2, 3, 4).
Crop and Pan would be more complicated, as they would require dealing with the possibility that the Underlay
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RWCox
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AFNI Message Board
It is possible to extract eigen-series from an ROI with various AFNI programs, but at this time 3dNetCorr doesn't have that ability built into itself.
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RWCox
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AFNI Message Board
A variation on Benjamini, Krieger and Yekutieli, applied voxelwise.
Note that the surname of the first author ends in "i".
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RWCox
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AFNI Message Board
What you want to do does not fix exactly into the AFNI analysis model, where we have a global "baseline" model (which includes the mean and slow drifts up/down), and we don't have a local "baseline" model.
Below is my quick jet-lagged outline of how you could do such an analysis in AFNI. However, there are probably not enough details here unless you are already a prett
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RWCox
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AFNI Message Board
That is a lot of overlapping questions to ask, and that makes it difficult to answer coherently. Also, since you do not provide the commands you used for analysis, I have to guess at what you mean.
"Can the cluster size threshold output of clustsim then apply throughout the entire brain (e.g., even in those slices that don't have data for all subjects)?"
If you have such gaps
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RWCox
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AFNI Message Board
So your problem is due to a change I made in the stopping criterion, that overlooked using a large maxlev. I have fixed that in the source code. But until AFNI is rebuilt, you can work around this by using the '-minpatch' option to say what the smallest patch size you want is. Use '-inilev' as before to specify where to start.
** bob cox
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RWCox
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AFNI Message Board
This effect is some annoying bug in OpenMotif and its management of the neighboring widgets that make up the threshold slider and the colorscale bar. I have tried to patch over this problem several times, but for some reason the patch started causing trouble with a recent AFNI build. I simplified the patch, as Paul described above, and Rick did an emergency build Monday night to push this change
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RWCox
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AFNI Message Board
I don't know why this is happening. I will have to try it myself. I made some changes to 3dQwarp recently, but I cannot imagine which one could cause this effect.
Since it takes a while to run 3dQwarp (as you know), it will be a little while before I can get back. And at this moment, I am in Lucca teaching AFNI, so that will slow things down as well.
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RWCox
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AFNI Message Board
My guess is that /Users/MRIdata/Ser3 is a directory, not a file. If that is the case, something funny seems to be happening.
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RWCox
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AFNI Message Board
There are no AFNI programs that use GPUs. The reason is that the programs (such as 3dQwarp) would have to be rewritten extensively to use a GPU, and that doesn't seem likely.
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RWCox
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AFNI Message Board
It would help if you could give the actual command you ran to get this error message, rather than just the message. Otherwise, we can't know how you got to that point.
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RWCox
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AFNI Message Board
I don't understand what you mean by "line/vein" artifact. Do you mean that you get some WM squished down to little tiny threads?
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RWCox
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AFNI Message Board
1) I would not use -detrend on the errts file - this option was intended only for use on original data for a quick look at the noise smoothness, and not for use on already processed data. However, I don't know why -detrend sometime affects the results markedly and sometimes does not.
It does not make any sense to average the 3 ACF parameters, which each represent something completely dif
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RWCox
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AFNI Message Board
I have made the change to @grayplot so it will use +orig datasets if +tlrc datasets are not found.
This change will be in the next binary build. If you send me email to robertcox@mail.nih.gov then I can email you a copy of this script to use immediately, since I can't predict when the n
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RWCox
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AFNI Message Board
It did not occur to me to make @grayplot work with +orig space outputs in afni_proc.py
I will modify it to check what the final "space" is and adjust the filenames it looks for to match.
WHEN? Perhaps this weekend.
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RWCox
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AFNI Message Board
At this moment, I'm trying to figure out how to avoid this problem, but the problem I've having now is that I cannot duplicate the issue.
However, I've added a message to inform the user when such 'minmax.1D' files can't be found, that the only loss is the '5percent.txt' files -- which I only put in there because one person asked for them, and because th
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RWCox
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AFNI Message Board
Program 3drefit can change values in the header. For example
3drefit -TR 2 StupidDataset.nii
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RWCox
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AFNI Message Board
This is annoying, and I have seen it before - when other people run ETAC, but not when I have run it. Probably because I use a Mac (mostly).
The failure to read these files means that the '5percent' files will not be produced (read the 3dttest++ -help output), but that is all.
What seems to be happening is conflict when the multiple instances of 3dttest++ spawned by the master pro
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RWCox
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AFNI Message Board
If you REALLY want to do prewhitening without regression against any task or regressors, 3dREMLfit cannot do that. However, it CAN do a very minimal regression without a task matrix from 3dDeconvolve. The minimal matrix is the single column of all 1s -- if you don't supply a '-matrix' option, this is what it will use. The result will be that the estimated mean is regressed from eac
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RWCox
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AFNI Message Board
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Pages: 12345