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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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And last night (27 Jan 2016), we automatically ticked up to version 16.0.01 with a rebuild of the binaries. As before the main AFNI web page http://afni.nimh.nih.gov/ shows the current build date and version number -- in the upper right hand corner.
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Emperor Zhark
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AFNI Message Board
These are hard questions, and I have to think about them for a while.
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Emperor Zhark
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AFNI Message Board
It's very hard to keep one's secret identity hidden.
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Emperor Zhark
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AFNI Message Board
I'll add that you can also use a dataset input string of the form
maskdataset+tlrc'<3..3>'
to specify that the dataset, after being read in, will (inside the program being used) get all voxel values 'v' that are not equal to 3 set to zero.
In general, datasetname'<a..b>' means to set all values outside the interval to zero after input. Th
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Emperor Zhark
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AFNI Message Board
For example, SPM and FSL use 1-sided thresholding for t-tests. I think they also use what I call NN2 clustering -- that is, voxels whose faces or edges adjoin are considered neighbors in the cluster-izing algorithm.
We give you lots of choices -- the price of which is that you have to understand what is going on in order to make a correct decision.
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Emperor Zhark
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AFNI Message Board
That looks good to me.
But how did you decipher my secret identity?
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Emperor Zhark
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AFNI Message Board
Assuming the mask dataset has each ROI marked with a different integer, you could do something like (using csh syntax)
3dhistog -omit 0 -unq U.1D maskdataset+tlrc > /dev/null
foreach uuu ( `1dcat U.1D` )
3dcalc -a maskdataset+tlrc -expr "equals(a,$uuu)" -prefix maskdataset.$uuu
end
\rm -f U.1D
For an ROI labeled with "3" (e.g.), you would get a dataset named mas
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Emperor Zhark
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AFNI Message Board
... which command should I use to threshold my group results?
Presumably you are going to threshold your group results in standardized 2x2x2 mm space that SPM uses, and inside the group mask "mask.hdr" (that is, voxels outside this mask will be ignored, even if above threshold). In which case, command A is the reasonable choice.
The other commands suffer from (i) not having a mas
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Emperor Zhark
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AFNI Message Board
Looking back at the change history, there was a change made on 13 Oct 2011 that affected the way the covariate matrix squared inverse was calculated. The diagonal elements of this matrix appear in the denominator of the t statistic, and so under some circumstances this could change the t-statistic -- but it would not affect the numerator, which is the 'overlay' value to which you allud
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Emperor Zhark
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AFNI Message Board
How are you looking at the datasets? The default application of 3dDFT is to produce complex-valued datasets. If you use AFNI to view the results, AFNI will show the magnitude of the complex dataset by default -- if you want to see the real part, you have to switch to that viewing mode. Given the .niml.dset suffix you are using, I suspect you are using SUMA to view the results. I'm not su
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Emperor Zhark
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AFNI Message Board
Is this a single task, or are there multiple tasks/conditions involved? The former case might be tractable, the latter sounds pretty hard.
In the single task case, you could setup your 3dDeconvolve analysis run. Then
analyze the same data repeatedly, adding various levels of the "-stim_times_subtract SS" option, where "SS" is the amount of time (in seconds) to subtract f
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Emperor Zhark
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AFNI Message Board
There is no fixed upper limit to the size of a data table in 3dttest++, so I'm not sure what's going on here.
Is this block below a direct copy of the output, without edits?
++ loading covariates
100408' in covariates file '
101006' in covariates file '
101107' in covariates file '
These messages are supposed to be in the form
** ERROR: C
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Emperor Zhark
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AFNI Message Board
3dQwarp is in a state of flux at the moment, so 5x5x5 might not work for you at the moment. Sorry, but I'm trying to evolve some changes, hopefully for the better. However, another "crisis" has arisen that has distracted from this question.
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Emperor Zhark
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AFNI Message Board
Newly Advertised
Tenure-Track, Tenure-Eligible Investigator
Computational Modeling, NIDA
(Review of Applications Begins: December 28)
The Intramural Research Program (IRP), National Institute on Drug Abuse (NIDA), a research component of the National Institutes of Health (NIH), Department of Health and Human Services (DHHS), is seeking an outstanding tenure-eligible or tenure-track scientis
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Emperor Zhark
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AFNI Message Board
What do you mean by "forcing the slope to be positive"? Do you mean that you want the best positive correlation with the ideal time series, versus the best absolute value correlation (the present method)?
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Emperor Zhark
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AFNI Message Board
At present, no.
3dttest++ has the -singletonA option, which does allow this type of one-vs-many analysis. But I haven't put this capability into 3dGroupInCorr yet.
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Emperor Zhark
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AFNI Message Board
When AFNI_redisplay_func_all() is called, the stream of events will eventually result in a call to AFNI_func_overlay() which is where the MRI_IMAGE for the actual overlay is created -- from the OLay dataset. The 'ovim' element you create will be lost at this point.
Why are you modifying the AFNI source code, anyway? If you really want to create a new form of overlay, the best way i
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Emperor Zhark
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AFNI Message Board
I forgot to mention the other change to the Clusterize report table -- the new linkRbrain button. Pressing this button takes the list of coordinates in the table and sends it to the linkrbrain.eu server, which will give back a list of noun phrases associated with that list of locations in the brain. This operation is somewhat distinct from the operations in SumsDB or NeuroSynth (available in AF
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Emperor Zhark
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AFNI Message Board
I have updated the interactive AFNI Clusterize, so that each cluster row in the table now starts with an on/off toggle switch. If you click the switch to "off", the cluster will disappear from the overlay.
Changing the threshold slider will cause all these switches to be turned back "on".
Another small change in Clusterize and its interaction with 3dClustSim tables: if
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Emperor Zhark
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AFNI Message Board
It is possible to do a little of what you want with the AFNI interface. To see how it is done, look at the file README.driver, and scroll down to the section labeled ** GRAPHS **.
Link to README.driver =
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Emperor Zhark
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AFNI Message Board
If you have some data to analyze with NO errors (in any data included in the analysis), you can do as James suggested to create a "timing" file with no times. Then you add the command line switch -allzero_OK to indicate to 3dDeconvolve that a regression model that has no data is allowed -- normally, it will freak out (i.e., print an error message and quit) when that situation happens.
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Emperor Zhark
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AFNI Message Board
What you want to do could be done with IM regression using TENT (or CSPLIN) basis functions, and then cutting out the relevant betas for each event in a script, most easily from the -cbucket output file.
However, it would be simpler (IMHO) to setup the separate model for correct vs. error trials and then do standard (non-IM) regression combined with the -iresp option to get the hemodynamic res
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Emperor Zhark
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AFNI Message Board
The AFNI header format does not allow for separate cluster tables for separate sub-bricks. What you are trying to do cannot be done at this time.
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Emperor Zhark
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AFNI Message Board
I don't see the motive for doing this. There are 2 time series regression programs involved.
3dDeconvolve does regression using ordinary least squares (OLSQ).
3dREMLfit does regression using generalized least squares (GLSQ), with REML estimation of the covariance matrix involved.
Your script would do GLSQ estimation of the motion effects and subtract those from the data. Then with t
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Emperor Zhark
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AFNI Message Board
We want to know which clusters are significant (multiple comparison corrected) at p < 0.05
So according to the alphasim result above, should we threshold the result maps in AFNI at a) 0.025 or b) 0.05 ( ie: 0.025 X 2 - to convert 2 tailed to 1 tailed)
First of all, you must be running an older version of 3dClustSim -- the program was changed in Feb 2015 to allow for the differences betwe
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Emperor Zhark
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AFNI Message Board
Sorry -- I forgot to start a rebuild last night, and just remembered now (11am in Bethesda). The rebuild is now started, and new binaries should be available by about 1pm.
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Emperor Zhark
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AFNI Message Board
So I added the new environment variable AFNI_USE_ERROR_FILE
If you set this to NO, then 3dDeconvolve.err will not be created. You can do this on the command line, via
3dDeconvolve -DAFNI_USE_ERROR_FILE=NO ...
or in the shell script somewhere before the program runs, or in your ~/.afnirc file.
This change is in the GitHub source repository now, and will be compiled into binaries overn
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Emperor Zhark
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AFNI Message Board
Not at the moment, but I could add an environment variable to turn this feature off. Stay tuned ....
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Emperor Zhark
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AFNI Message Board
I guess that you prepared this file on a Windows machine, perhaps in Word -- where the character encoding is not necessarily ASCII, so what you SEE is not what you GET in the file. You'll have to convert the file to plain text.
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Emperor Zhark
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AFNI Message Board
Try setting environment variable AFNI_QUIET_STARTUP to YES -- that should shut up most (but probably not all) such messages.
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Emperor Zhark
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AFNI Message Board
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