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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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3dQwarp (the engine inside our nonlinear warping scripts) also has two options that let you give extra weight to registration in a particular small region. From the -help output of 3dQwarp:
-wball x y z r f =
Enhance automatic weight from '-useweight' by a factor
of 1+f*Gaussian(FWHM=r) centered in the base image at
DICOM coordinates
by
RWCox
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AFNI Message Board
There is also program 3dmaskSVD.
And the related (slower) programs 3dLocalPV and 3dLocalSVD -- which give you the eigenvector(s) of the time series from a neighborhood around each voxel.
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RWCox
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AFNI Message Board
QuoteWould someone happen to know how many neighboring volumes are used to interpolate the censored volume and what would happen in the case outlined above (i.e., if two or more consequent volumes in a time series are outliers)?
The two closest neighboring volumes (in time) are use -- one before and one after, and the interpolation used is linear. For example, if time indexes 1 and 5 are kept,
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RWCox
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AFNI Message Board
As the instigator/inventor/implementor of the ETAC approach, I have to say that I've never tested the accuracy of the tests for the false positive rate (FPR) for covariate estimates. It occurred to me to do so, and I even wrote scripts for that purpose. But didn't carry those tests out.
What Anderson Winkler makes intuitive sense to me, but I never got that far in my implementation.
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RWCox
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AFNI Message Board
If you are dealing with human brain images, and are willing to run somewhat longer CPU times, then the @SSwarper script with the "-skipwarp" option might be best -- as a preprocessor. Then run 3dAutomask on the anatSS.SUBJECT-ID.nii output.
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RWCox
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AFNI Message Board
For example, when I try a command similar to yours, I get:
++ 3dttest++: AFNI version=AFNI_22.0.21 (Mar 21 2022) [64-bit]
++ Authored by: Zhark++
++ Number of -Clustsim threads set to 8
++ option -setA :: processing as SHORT form (all values are datasets)
++ have 28 volumes corresponding to option '-setA'
++ option -setB :: processing as SHORT form (all values are datasets)
+
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RWCox
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AFNI Message Board
In what way doesn't it work? Do you get any Warning or Error messages? In situations like this, it helps a lot if you can copy/paste the screen output text from the program to help diagnose what exactly happened.
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RWCox
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AFNI Message Board
Datasets are sorted in the following order (going by memory):
AFNI formatted datasets -- those datasets which are marked as having an "anatomical" type AFNI formatted datasets -- those datasets which are marked as having a "functional" type NIfTI formatted datasets ANALYZE formatted datasets (very rare now; controlled by environment variable AFNI_ANALYZE_DATASETS) CTF .m
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RWCox
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AFNI Message Board
I will add to Daniel's customary excellent advice -- whatever you do, look at the two brain images after alignment. You can flip between them easily in AFNI by setting one as the Underlay and the other as the Overlay, and then using the 'u' keypress (with the mouse cursor focus in the image viewer) to flip them -- with the 'See Overlay' off. This method is a good way to
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RWCox
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AFNI Message Board
This could be done with the following steps:
Align the twins' brain images approximately with 3dAllineate, so that they are "pretty close". Use 3dQwarp -plusminus to warp the two previously aligned brain images towards each other -- to "meet in the middle".
If you want them to be close to MNI space, then in step 1 you should align them to the MNI template instead of t
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RWCox
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AFNI Message Board
I have been unable to reproduce your errors with synthetic datasets.
My only 2 suggestions are
Make sure you are using the latest version of AFNI binaries. Use 3dREMLfit instead of 3dDeconvolve if possible.
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RWCox
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AFNI Message Board
I made up some large data (120+ GB) in the form of 250 500 MB datasets, and tried to run 3dDeconvolve on them auto-catenated on the command line. The program was able to read all the data in, set up the regression matrix, and start the work -- but it was taking so long, I killed the job after a while before going to bed.
However, this convinces me that I need more information from you.
The se
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RWCox
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AFNI Message Board
I will have to try something, since it is weird that it works for "small" datasets and fails for "large" datasets.
Please give me the information about your datasets listed below: Dimensions (grid points in each direction, including time) Dataset "type" (floats, shorts, ???) Largest number of time points where 3dDeconvolve seems to work in your experience Numbe
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RWCox
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AFNI Message Board
These are hard questions to answer, for a couple of reasons.
First, it has been a LONG time since I used periodograms seriously (say 1985).
Second, since I don't have access to your data, I'm flying blind here.
Here's my first stab at suggestions, in no particular order:
Look at the outputs of 3dPeriodogram to see what could be causing the weirdness in the fit. Consider usi
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RWCox
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AFNI Message Board
The output of "3dFDR -help" has some explanation. The method is the basic B-H technique (voxel-wise, not cluster-wise), with an adjustment for estimated fraction of "true negatives". As Rick says, a mask is important to cast out non-brain voxels from the considerations.
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RWCox
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AFNI Message Board
These "isn't long enough" messages are caused by the .sdat files written during the 3dttest++ randomization runs being truncated somehow. Not empty and not non-existent, because those are different messages.
But how that file truncation happened, I don't understand. The only thing I can think of is that the disk storage is full, but that seems very unlikely, and you would a
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RWCox
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AFNI Message Board
I can't say anything about the 3dGroupInCorr problems right now -- it seems to be some network/security thing. Unless it is connecting to suma instead? However, unless you are superuser (root), you don't have permission to kill jobs belonging to other users.
OK, one 3dGroupInCorr thought -- try using the -NOshm option, which will avoid the default attempt to use shared memory instead
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RWCox
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AFNI Message Board
I'm not *quite* out yet, but in a few moments.
I don't see anything wrong with your GUI InstaCorr usage -- after it says "ready for work", it should work -- and it does on my computer just now. So that is a mystery to me.
The GroupInCorr screen output also says it is ready (connected). The only thing I can think is that you are running 2 copies of AFNI -- perhaps one is
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RWCox
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AFNI Message Board
I'm glad your problem is fixed. As usual in life, that means you can now rush ahead to the NEXT problem.
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RWCox
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AFNI Message Board
To be clear, you want to compute separate betas for each run, for the onset_C_test.txt file, where each row has the stim timings for one run? But for the other stim files, the betas are for all runs and you are cool with that?
If the answer to both questions is YES, then you have to split onset_C_test.txt into 16 separate files. There are two reasons:
The timing file for EACH -stim_times opt
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RWCox
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AFNI Message Board
Daniel Glen Wrote:
-------------------------------------------------------
> ALIENS!
Obviously. Any other suggestion would be absurd.
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RWCox
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AFNI Message Board
And another strange thing, obviously very ancient as I came across it in Egypt.
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RWCox
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AFNI Message Board
Funny you should mention "AFNI" and "rocks" in the same sentence. See the attached picture, which is a strange geological phenomenon I chanced upon in the Grand Canyon some years ago.
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RWCox
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AFNI Message Board
OK, the error is fixed (I hope) in the latest release of AFNI = AFNI_21.2.02 (just released now). There was a problem reading files larger than 2 GB -- in a different place, this time.
It takes about 30s to read your 2+ GB file, which has the data stored in binary format. I converted it to a text-only file, at 5+ GB, and that took 150s to read into memory -- showing the increased efficiency of
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RWCox
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AFNI Message Board
Does this happen if you use "better" values for -pblur, or just eliminate the -pblur option? Please re-run with the "-verb" option, which will print out more verbose progress messages, which might help (some). Is there anything in your ~/.afni.crashlog with more information about the crash?
Since the cost function is the default, the value shown doesn't seem "t
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RWCox
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AFNI Message Board
How much "rest" time occurs before and after the onset of the continuous stream of stimuli (that is, at the beginning and end of the imaging run)? Probably not much, I'd guess.
In this situation, IMHO you can only reasonable find the difference between the linguistic condition #1 and the foil condition #2 -- that is, you can't find "linguistic only" activation, ju
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RWCox
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AFNI Message Board
So it stops AFTER writing 2.8 GB of the output file?
How big is a completed file with 9 input runs? Then multiply by 29/9 to estimate the size of the desired file?
The result has been computed in memory, and the problem is converting it to the .niml.dset format and writing that to the output.
One possibility is that the output function is keeping track of bytes output into a 32 bit integer
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RWCox
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AFNI Message Board
If you wish to analyze such a large dataset as a whole, there are some options in AFNI. Most of them will require running on a system with enough RAM to hold the entire dataset easily. However, if you are industrious enough, you can break the dataset into pieces to reduce the memory footprint required at any given point.
No matter what you do, you will have to manage the analysis yourself, as
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RWCox
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AFNI Message Board
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