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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
Hi, Sam-
Great to hear, and thanks for letting us know.
--pt
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ptaylor
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AFNI Message Board
I might have thought the 1-sided vs 2-sided (or, for clustering, like "bi-sided") might be the issue, but it looks like the missing cluster had the same size as several others (6 voxels). Juuuust checking that there wasn't one cluster that would be seen by scrolling down in the cluster report? Also, knowing the threshold in each case would be useful (did you provide a p-value and
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ptaylor
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AFNI Message Board
Hi, Sam-
Great, glad the IT was accommodating so quickly.
Thanks for sending those images---that helps show that the initial overlap is quite good, both initially and after the center-of-mass shift (perhaps some center-of-mass alignment had already even been done, esp. judging by the input filename? Fine.). Actually, that was the main thing that I thought might be going awry here. The ti
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ptaylor
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AFNI Message Board
Thanks, that is mildly illustrative that the situation is: adding the covariate makes that swath have notably larger-magnitude values than the surroundings, rather than it shrinks values outside the swath.
I am still not sure what would cause this. Some kind of outlier-ish interaction with values? Might have to look at the data to investigate further.
-pt
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ptaylor
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AFNI Message Board
Wow, powerful covariate! And to check one further thing, the range in the colorbars is the same, I guess?
That is an oddly focal change to have with the covariate inclusion. Hmm....
--pt
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ptaylor
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AFNI Message Board
Hi, Lena-
I think the issue might be that if you are using a dataTable file, the contents of that file should not have a quote around the subbrick selectors, nor does there need to be the continuation-of-line characters "\" at the end of each line.
Note that the syntax of your current table---*with* those apostrophes and "\"s---would be correct if being used directly as
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ptaylor
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AFNI Message Board
Hi, Lysianne-
Hmm, interesting. What do the images look like unthresholded?
--pt
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ptaylor
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AFNI Message Board
Hi, Ian-
Glad it got sorted.
I'll just note that using conda/miniconda to make a local environment (I use this to manage Python on my own systems) is useful, modular and doesn't require sudo/admin privileges. There are other ways to go, certainly, and it sounds like you are set, but I note this for anyone with similar constraints reading this thread. Here are notes about using m
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ptaylor
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AFNI Message Board
Hi-
AFNI I/Os BRIK/HEAD format, as well as NIFTIs. If you would like the output to be a NIFTI file, then just include that extension in the output file prefix, such as:
3dLocalstat -nbhd 'SPHERE(3)' -stat mean -automask -prefix DSET_OUTPUT.nii.gz DSET_INPUT
Just to note, there are some useful getting-to-know-AFNI and general MRI/FMRI analysis teaching materials here:
https://
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ptaylor
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AFNI Message Board
Hi, Naail-
OK, glad that sorted things.
I will just note that if you are processing FMRI analysis with using surface projection, then afni_proc.py can help with a lot of the details:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/programs/alpha/afni_proc.py_sphx.html#example-8-surface-based-analysis
--pt
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ptaylor
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AFNI Message Board
I think that would be good to do, yes.
I don't think you can install it just with conda, say.
--pt
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ptaylor
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AFNI Message Board
Hi, Sam-
Thanks for providing that.
The CentOS depending list is here:
... and includes Xvfb. Are you running on a managed software system, or on one where you have sudo/admin privileges to install software?
I also see this failure message:
** failed to load module matplotlib.pyplot
... which will be problematic at times. Your Python of choice comes from miniconda:
/cubric/da
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ptaylor
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AFNI Message Board
Hi, Philipp-
This is the section of the AP help on bandpassing, for reference:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/programs/alpha/afni_proc.py_sphx.html#resting-state-note
We should clarify terminology to start:
In resting state FMRI, when people talk about "bandpassing during processing", they are pretty much always referring to low-frequency fluctuation (LFF) bandpa
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ptaylor
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AFNI Message Board
Hi, Sam-
There are a couple things to note. The first error message that program produces is:
** ERROR: Xvfb -- not found in path -- program fails
.... which means that the automatic QC image generation cannot occur. It would be good to fix that issue, since looking at the QC images was going to be my first question to help address the other/main code crashing.
Could you please copy+pas
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ptaylor
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AFNI Message Board
Rockin'.
I will note that there is 3dpc in AFNI, as well, for PCA decomposition of a 4D dataset, in case that is also useful.
--pt
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ptaylor
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AFNI Message Board
Hi, Naail-
Hmm, that is a weird number of nodes to have---198,259 instead of 198,812. Fascinating.
This would list out the number of *niml.dset files in the current directory in time reversed order, showing the number of dimensions each dset has:
3dinfo -n4 -prefix `\ls -tr *niml.dset`
Perhaps you could see which dset that should have 198,812 has the wrong number, as a start.
Is thi
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ptaylor
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AFNI Message Board
Hi, Jacob-
I think the code syntax is incorrect. The input filename has to be at the end of the list of command line options and arguments, like:
3dLocalstat -nbhd 'SPHERE(3)' -stat mean -automask -prefix DSET_OUTPUT DSET_INPUT
How does that work for you?
--pt
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ptaylor
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AFNI Message Board
Hi, John-
The datasets have a property of "AFNI view space" (av_space) and "space"; these map onto the qform_code and sform_code values in the NIFTI header, but are slightly different. The av_space values are typically +orig (for datasets in original or at least non-standard space) and +tlrc (for datasets in *any* standard space)---so that av_space is about the general spa
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ptaylor
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AFNI Message Board
Hi, Clement-
It is always good if you can set up this kind of workflow with a very clear example to test+verify it on first.
You can also do something like use 3dcalc to make 1 hemisphere clearly demarcated. For example, the following will output a copy of the input dataset where all values with x-coord>0 are replaced by 1s:
3dcalc -a DSET -expr 'step(x)*a + not(step(x))*1'
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ptaylor
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AFNI Message Board
Hi, Clement-
I'm a little confused. I guess the main question is: do you know which hemisphere is the participant's, say, left side of the brain when you open the initial/raw/unchanged dataset? If the answer to that is "yes" (and I hope it is), then it should be fine to verify the final choice of re-orientation.
There are different paths to go through with the alterin
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ptaylor
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AFNI Message Board
I think the main aspect is: while it seems reasonable to restrict the voxel analysis to GM (fewer voxels, about 1/3 of the brain volume -> less adjustment for multiple comparisons), the practical reality of the geometry of GM is that the analyzed region becomes less of a simple volumetric shape. Both these kinds of cluster simulations and random field theory-based corrections depend on the s
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ptaylor
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AFNI Message Board
Hi-
Thanks for sending the mask. I show it overlaid on the one I had been testing---it is indeed a bit narrower, esp around the ventricles. I don't know that that is an inherent problem, but those narrow regions are kind of non-ideal for the 3D cluster calcs and smoothing. It might just be part of life when using a GM mask. When I ran with just the default 10,000 iterations, the clust
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ptaylor
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AFNI Message Board
Hi, Giuseppe-
If your vector of interest happens to be one of the eigenvectors of a tensor, then you are in luck, because there is an eigenvalue for each one, that provides detailed information on the diffusivity in that direction.
It might be helpful to check out the AFNI Bootcamp presentations on DTI:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/educational/bcamp_2017_10_nih.html#dti
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ptaylor
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AFNI Message Board
There is some stochasticity in these calculations, so they will be likely to vary a litttle bit across runs. 3dClustSim calcs are also generally intended to be run in more spherical, whole-brain masklike masks, as well. Having a mask that is composed of set of linear-ish structures with complicated boundaries can affect some of convergence, I would guess. I mention this because from your filen
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ptaylor
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AFNI Message Board
Hi, Ian-
I think you will be happier with the full pythonic version, yes! But indeed, we need to fix that error message.
So, the default package manager in Ubuntu 20.04 (Aptitude) distributes a version of Matplotlib, 3.1.2, that contains this error when trying to make JPGs:
I don't know why they haven't fixed it, and it is the root cause of the error here.
The good news: t
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ptaylor
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AFNI Message Board
Hi, Angelika-
Indeed, your input EPI should be in native space, not a standard space, before processing starts.
There are 2 ways it might *appear* to be in standard space:
1) It *is* actually in standard space.
2) It is a NIFTI file, and it has an qform_code and/or sform_code value in its header that is the dreaded "ambiguous space" one that was somehow allowed in the NIFTI stan
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ptaylor
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AFNI Message Board
Hi, Clement-
Glad to know the purpose of this---de-sphinxifying.
The reason for 3dresample is that I find it easier to think about using the change in dataset orientation for the purpose of desphinxifying when starting from a "simple" orientation where the L-R axis is in the spot of the x-coord, the A-P axis in that of the y-coord and the I-S axis in that of the z-coord. 3dresamp
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ptaylor
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AFNI Message Board
Hi, Clement-
I guess you are asking both if *you* are right and if your dataset's *right hemisphere* is on the right?
Can I ask, is this possibly a sphinx-position dataset that you are aiming to un-sphinxify?
I guess I might do this in steps, because it sounds like you want to:
1) remove obliquity from the dataset
2) change definition of planes (so, what is currently an axial slic
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ptaylor
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AFNI Message Board
Hi, Sam-
You might have already seen these pages, but here is a bit about the D99 v2.0 that you are using:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/nonhuman/macaque_tempatl/atlas_d99v2.html
... and we also have some animal MRI processing demos:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/nonhuman/macaque_demos/main_toc.html
... that include running both @animal_warper and afni_pro
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ptaylor
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AFNI Message Board
Hi, Sahithyan-
Ah, thanks for pointing that out. I have just updated those links in the documentation here:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/template_atlas/sswarper_base.html#reference-templates-for-sswarper
Please let us know if that doesn't work.
For citing, we usually just cite the workhorse nonlinear warping program at the heart of @SSwarper, which is 3dQwarp, whos
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ptaylor
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AFNI Message Board