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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:
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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
Results 4171 - 4200 of 4524
Hi Wolfram,
How much blur is in the original data depends on the scanner
and protocol. But it is generally more than zero, which means
the applied blur will be less than the resulting (estimated)
blur.
When running 3dFWHMx, be sure to apply a mask, and process
just one run at a time. You might consider what afni_proc.py
does with it, when you ask to estimate the blur.
Note also th
by
rick reynolds
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AFNI Message Board
This does not sound too special. Note that 3dROIstats works like
3dmaskave, except that it will output one result per ROI. So you
could get average time series of many ROIs with one command.
The correlation matrix is something that is commonly done, though
I do not know what people use. I will try to recall to ask Hang Joon
how he does that.
In any case, note that for just computing
by
rick reynolds
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AFNI Message Board
Hmmm, I don't understand how things were different between
running Dimon by hand and doing it as a script then.
But consider the -rev_org_dir option. That should reverse the
file order generated by -dicom_org.
- rick
by
rick reynolds
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AFNI Message Board
Hi Cathy,
Consider using 3dBandpass. Also, if you plan a regression,
note that polynomials are often used to model that drift, and
so you would not need to use any Fourier filter. Also, beware
of time breaks between runs. Each run should be filtered
separately.
Also, consider describing what you are attempting to do
overall (what sorts of processing). Maybe there is a higher
level
by
rick reynolds
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AFNI Message Board
Hi Kyunghee,
Note that 3dresample will destroy any oblique matrix.
Why are you not having afni_proc.py do this? See example #6.
I see that you have not set up your path. You will not be able
to run scripts using the current binaries unless your path is
properly set up.
- rick
by
rick reynolds
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AFNI Message Board
Hi Chris,
For the record, AFNI has matlab functions in the afni_matlab.tgz package
that include reading and writing datasets. That seems easier than going
through 3dmaskdump.
Hopefully you are on planning to use any Fourier transforms on the shortened
datasets. It might be worth telling us your plans, in case we know how to do
some things.
Creating a time series without censored T
by
rick reynolds
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AFNI Message Board
Maybe you have old GERT_Reco_dicom files there,
and are running the old ones and not the new ones.
I suggest adding the Dimon option -gert_create_dataset,
so that you do not need to run GERT_Reco_dicom yourself.
That will at least remove one command from consideration.
Start by deleting all of the old Dimon results, too, just to
keep things clean.
- rick
by
rick reynolds
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AFNI Message Board
Hi Juen,
What is the effect of added -dicom_org?
- rick
by
rick reynolds
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AFNI Message Board
Hi Lisa,
The exact estimate for the alpha value of a single cluster
(that size or bigger per volume) would have to come from the
3dClustSim table directly. Only approximations are given in
the GUI.
- rick
by
rick reynolds
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AFNI Message Board
Hi Shant,
If you want the modulation contrast, that would be:
'SYM: incong[1] -cong[1]'
Take a look at the Decon link in my previous response
details about that.
- rick
by
rick reynolds
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AFNI Message Board
Hi David,
Unfortunately, if the images appear upside-down (as in I and S
are flipped), then it is not as simple as changing LPI to RAI
(since the 'I' is not correct).
Your thought of using some .nii dataset as a geometry parent
for the analyze dataset is good, except that it seems the
analyze datasets are simply not in the same orientation as the
original DICOM images. So su
by
rick reynolds
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AFNI Message Board
Hi Lauren,
Without seeing your actual processing scripts (and even
after seeing them), it is very hard to guess what might be
going on. It could even be as simple as something you are
doing in the afni GUI, to only show positive results.
I suggest using afni_proc.py for the single subject processing
(example #5 if you have physio data, and example #9 if you
do not). Then take the out
by
rick reynolds
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AFNI Message Board
Hi Shant,
It would be very helpful to see the actual 3dDeconvolve command.
Note that the output from the command makes explicit what the
contrasts are computed from, for verification.
But if you have condA and condB as your labels, and if they both
have 2 regressors (via AM2), the condA-condB should be the sum
of the mean and modulated responses for A minus those for B.
You have not
by
rick reynolds
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AFNI Message Board
Hi Lisa,
I don't suppose you are using afni_proc.py for single
subject analysis, are you? It can do this, letting you
basically copy the command for the group level result.
The statistics dataset is the one you want to cluster.
- rick
by
rick reynolds
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AFNI Message Board
Hi Sarah,
It would be useful for you to answer the same questions
that Kyle did. What is the output from these commands:
which python
python -V
- rick
by
rick reynolds
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AFNI Message Board
There is at least one problem that would lead to such an error
at the end of your command.
You have "3 3 SWL_highvslow" without any -abmean, option,
presumably.
- rick
by
rick reynolds
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AFNI Message Board
You should be able to get the exact same results with
3dDeconvolve. In either case, it is just a regression.
The components can be regressed using -stim_file options.
Maybe start by replicating your results with 3dDeconvolve,
then you will know how to continue.
If you are unsure, post the 3dfim+ command.
- rick
by
rick reynolds
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AFNI Message Board
Hi Amanda,
No, the sigma resid is the standard deviation of the residual time series.
What you need is the residual time series, itself. The 3dfim and 3dfim+
programs output neither the fit time series nor the error (residual) time
series.
We are not really maintaining those programs much anymore, since
3dDeconvolve is a much more useful program.
May I ask why you are not using 3dDe
by
rick reynolds
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AFNI Message Board
Hi Jie,
Using -sigma seems to work better than -Niter (which you are not
really using either, since you pass -1 as the parameter).
Try -sigma 1.0 (a little lower if it is too fast, or higher if too slow)
and remove -Niter.
- rick
by
rick reynolds
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AFNI Message Board
Hi Colm,
The filelist: style input essentially catenates the input
datasets into one big one, like sending them to 3dTcat.
So this method is not appropriate for 3dMean, since it takes
a list of datasets as input to begin with. And if the inputs
have multiple sub-bricks, the output is the mean per sub-brick
(i.e. it would have the same number of volumes as the input).
If you need to
by
rick reynolds
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AFNI Message Board
Hi JoJo,
Aug 15 is not new enough. Paul's announcement is from Aug 27.
Please update your binaries to try this out:
@update.afni.binaries -defaults
- rick
by
rick reynolds
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AFNI Message Board
Hi Liana,
I have never encountered a problem with the -regress_polort option,
and it seems to be working fine now. If it is not working for you,
it would be helpful to see your command line.
Yes, if you use '-regress_polort 2', then '-outlier_polort 2'
makes sense.
To make things simple, please feel free to send me your resulting
proc script via email (assuming y
by
rick reynolds
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AFNI Message Board
Hi JoJo,
They should be in the most recent binaries.
You didn't say what you are using. What are the 2 lines
of output from "afni -ver"?
- rick
by
rick reynolds
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AFNI Message Board
Hi Marwa,
Why the avarages are negative I will leave to you, but that they
are small is not such a big surprise.
1. Because correlations are from normalized vectors (unit weights
of 1.0), the 1/-1/0 multiplication will lower the maximum
result. In particular, the fraction of non-zero TRs will be
an approximate limit on the resulting R-values. And when R is
less than 0.5 (
by
rick reynolds
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AFNI Message Board
Hi JoJo,
The z-scores should be directly convertible to p-values, and
the afni GUI should show the p-value in the threshold slider
bar. So set your threshold in the GUI based on the p-value.
The q-values are not added automatically, but can be done by
you (again, still using the afni GUI). Right-click on the
threshold title (e.g. Z-t, if you are thresholding on the
resulting z-scores
by
rick reynolds
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AFNI Message Board
Hi Jatin,
That warning looks like a mistake to me, in that it includes
the input files. Does that program run anyway? It does for
me (since it is just a warning).
- rick
by
rick reynolds
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AFNI Message Board
Hi Becky,
I think you only get to use one "Insta" function at a time.
So to cluster, you must actually save the resulting dataset.
Via the live 3dGroupInCor, use:
Define Datamode -> SaveAs -> OLay
or you can do what we have been doing, use the -batch
option to 3dGroupInCor to create resulting datasets,
rather than via surfing through the afni GUI. With the
-batch
by
rick reynolds
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AFNI Message Board
Hi Melissa,
That seems to be a leftover from our server upgrade.
It has been fixed and updated.
Thanks for pointing it out!
- rick
by
rick reynolds
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AFNI Message Board
Hi Lauren,
You do not seem to be having any software problems at all.
As you have noticed, the way to control the voxel size is via
the -volreg_warp_dxyz option. Since it seems to bring your
computer to a grinding halt, it means you do not have enough
RAM for such an analysis. Note that going from 3.5 mm^3 down
to 1 mm^3 increases the size of the datasets by a factor of
approximately
by
rick reynolds
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AFNI Message Board