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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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Hi Robin,
Sorry for getting a bit distracted.
I was not expecting you to run 3dDeconvolve on a 4D dataset, ever, but to do something like:
- extract an ROI average time series of choice
(the realtime plugin can send this (or multiple)) to an IP address
- regress out the motion parameters (and polort) on the full time series
(run 3dDeconvolve on the 1D average)
- perform
by
rick reynolds
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AFNI Message Board
To be sure, is this regression and difference being done just within the ROI mask? Are you taking an ROI average, regressing out motion, and then using the resulting TR differences for feedback?
If so, consider regressing the motion parameters from the entire ROI average time series, not just from 13 TRs. Only after this might you extract values for the 13 time points of interest, using the
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rick reynolds
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AFNI Message Board
Indeed, that seems totally normal.
At 13 time points, you have half as many regressors as time point. The linear regression will in general look very noisy at the beginning (at least one of the motion regressors will probably fit that gentle rise that you are looking for), and will start to stabilize after sufficient time to have useful variance in the more "ideal" time series you a
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rick reynolds
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AFNI Message Board
Hi Cesar,
This might be another reason for you to consider compiling on your ARM system.
The R programs (like 3dMVM) are scripts that run R and load our compiled R_io.so library for dataset I/O. That version of AFNI has R_io.so linked to an Intel version of the build machine's R library.
But since 3dMVM is a script, in your case it is running an ARM version of R, and that is refusi
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rick reynolds
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AFNI Message Board
Thanks for sending the files. Indeed, they have non-printable characters in them, meaning they are not in pure ASCII text format.
You can use file_tool to fix them, for example. But it would be good to figure out editing methods that will not lead to this. It can cause trouble in scripts, too.
For now, you can test a file using something like:
file_tool -test -infile TIMING_FILE
A
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rick reynolds
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AFNI Message Board
That is strange. Would you please email me one or more of those timing files? Click on my name.
- rick
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rick reynolds
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AFNI Message Board
Hi Sahil,
There is currently no ability for afni_proc.py to pass FSL-style timing files. That is something I would have to ponder.
However timing_tool.py should be able to convert them. See Example 18 (a,b,c,d) in the timing_tool.py -help output.
- rick
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rick reynolds
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AFNI Message Board
Hi Jenna,
There is no such option at the present, sorry. It would be conceivable to add, though it is not an option we would recommend so highly.
- rick
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rick reynolds
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AFNI Message Board
What command gave that error? Can you show more details (or send me the output.proc* text file via email)?
It is hard to tell, but I wonder if there is some regressor file that some program could not read...
- rick
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rick reynolds
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AFNI Message Board
Hi Jonathan,
Dimon can output NIFTI, but I do not believe there is any mechanism to do so in the realtime plugin. If that is important, it could probably be added (though there are actually many potential datasets that it could write).
- rick
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rick reynolds
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AFNI Message Board
That's good news and surely a big relief, thanks!
- rick
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rick reynolds
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AFNI Message Board
I suggest not removing those rm_* files, so that you can verify what is in them when it fails.
Also, consider running the script via "tcsh -x", just to capture all the commands and output. That might have a lot of output, but should make debugging much easier.
- rick
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rick reynolds
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AFNI Message Board
Thanks. That has been quite the group effort, and is still a work in progress for the moving target that is macos... :)
- rick
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rick reynolds
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AFNI Message Board
Hey there Z,
Set the R version of it, R_LD_LIBRARY_PATH, as in scripts like 3dMVM.
export R_LD_LIBRARY_PATH=$(R RHOME)/lib:$HOME/abin:/opt/X11/lib/flat_namespace
Hopefully I have that syntax correct...
- rick
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rick reynolds
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AFNI Message Board
For that, I would still not include the tlrc block. You can get everything aligned to the vr_base EPI, including anat followers.
And then a completely separate step could be to compute a standard space warp via @SSwarper (using anat_w_skull), say, to invert and pull atlases back to orig space with.
Does that seem reasonable?
- rick
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rick reynolds
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AFNI Message Board
Indeed, as Paul notes, though afni_proc.py could likely be reasonably fixed to handle that, it seems just begging for trouble (in terms of both the complexity of afni_proc.py itself, and of people running it correctly). So my inclination for a "fix" would be to simply have the program error out, meaning you could not do it anyway.
Out of curiosity, why are you inclined to run the an
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rick reynolds
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AFNI Message Board
The fix for this went in and should be built and distributed to the afni server. So please feel free to update your binaries and see if it works again.
Thanks!
- rick
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rick reynolds
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AFNI Message Board
Hello,
Sorry for being slow, it was a while before getting around to debugging this.
It looks like 3ddot just happens to not like how linking is altered to be local. It just seems to be that one program in the entire distribution that fails.
I will fix this an run an updated build.
Thanks a lot for bringing it up!
- rick
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rick reynolds
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AFNI Message Board
Hi Tessa,
Just as a follow-up to others reading this thread, Tessa and I have looked into this and found that there is a bug in 3dDeconvolve when using -stim_times_IM for a regressor class that has no events. It is not such an odd case - one can see the use of IM in the case of missing or incorrect reponses, say, and then imagine that for some subjects, there might not be any such events. Ha
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rick reynolds
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AFNI Message Board
Hi Julien,
Would it be reasonable to use 3dcalc -expr 'argmax(a,b,c,...)' to get the index of a maximum R^2 result from 3dDeconvolve? That should be the same thing, but with the benefit of having all of 3dDeconvolve available. It would just take that one extra command, assuming 3dDeconvolve is run with -rout.
- rick
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rick reynolds
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AFNI Message Board
Hello,
Sorry, but I am still a bit confused.
You say that the ANT_WIN_VS_NOWIN contrast corresponds to Win ($1 and $5) vs No Win ($0). However ANT_WIN_VS_NOWIN seems to be defined as a simple contrast of 'WANT -W0ANT', suggesting WANT is itself Win ($1 and $5), and No Win $0 is -W0ANT (that part seems reasonble).
Would you be able to clarify 'Win' more? Exactly wha
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rick reynolds
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AFNI Message Board
Hi Tessa,
After looking at this in some detail, while still a bit confusing, it seems that the apparent full-volume stats are coming from inclusion of the compcor regressors. If those terms are not included in the model, the results look more as expected (though I do not know exactly what to expect from your analysis).
Getting the proper AM stim types and such would be good, but I do not t
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rick reynolds
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AFNI Message Board
Hello,
It looks like 5 of the 6 extra symbolic contrasts (SYM) are simple pairs as you describe, with only contrast 4 being a difference in means.
But to be sure, would you please specify the exact labels that correspond to wins($1) and wins($5), and similarly for loss?
It is hard to tell with any degree of certainty.
Thanks,
- rick
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rick reynolds
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AFNI Message Board
Hi Tessa,
Please feel free to create a tgz package with that information, including the *.xmat.1D file, and send that to me.
Click on my name for the address.
- rick
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rick reynolds
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AFNI Message Board
Hi Will,
You can probably check the libgsl version via:
ls -l /usr/lib/x86_64-linux-gnu/libgsl.so.*
Then link to the existing file.
For openmotif and libGLw, maybe try:
sudo apt-get install -y libmotif-dev libglw1-mesa-dev
- rick
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rick reynolds
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AFNI Message Board
Hi Philipp,
I do not see where the correlations are being computed here. Are the correlations across subjects, and one correlation per voxel, or is this a spatial correlation (e.g. 3ddot -demean)?
Either way, it might make sense to do this in volume space.
- rick
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rick reynolds
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AFNI Message Board