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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
Results 241 - 270 of 2305
Hi, Maya-
Your system looks set up AFNI-wise, though that is over a year old---I would probably run:
@update.afni.binaries -d
to update it.
Your system appears to only have Python 2.7 on it, so it would only be able to run the old meica (Kundu et al.), at present. If you wanted to run the more modern meica (Du Pre et al.), you should definitely update your AFNI, as above; you would t
by
ptaylor
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AFNI Message Board
Hi, Maya-
Hmm, that is surprising. What is the output of:
afni_system_check.py -check_all
?
Also note that the combine_method you are using, "tedana" is the older one from Kundu et al; that doesn't have a separate QC HTML block that is automatically created for the MEICA part. The newer MEICA from the 'tedana' group (Du Pre et al; here: ) would be selected wit
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ptaylor
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AFNI Message Board
Philipp-
This implementation doesn't have a way to adjust the binning. I guess "mean padding" the time series would be one way to go, but I have not tried that.
--pt
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ptaylor
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AFNI Message Board
Hi, Philipp-
Well, it's not a bug, it's a max buffer length defined in the code. It determines the maximum number of columns a *.1D file can have and still be read in.
This means that you have a *single line* with over 5M values---I guess each of your datasets is a time series of considerable length. Can I ask what you are aiming to do with this gargantuan line? Is there a way
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ptaylor
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AFNI Message Board
Ah, right. If it's any consolation, I was actually using "#!/bin/bash" as the shebang in my testing, not just "#!/bin/sh", which I had initially put when I was writing from a different computer... Sorry for the confusion.
--pt
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ptaylor
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AFNI Message Board
Josh-
Yes, all your major shells (bash, zsh, tcsh/csh) should be set up by the @update.afni.binaries install.
We often use tcsh for scripting, which does not have this issue.
--pt
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ptaylor
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AFNI Message Board
And as a followup, the crash is happening because of the script's shell not knowing the DYLD library, so adding the following to the top of the bash script would also prevent the crash (this is what ~/.bash_profile gets set to include):
export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:/opt/X11/lib/flat_namespace
Again, I think this is a Mac-specific issue, when using bash or zsh. The startu
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ptaylor
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AFNI Message Board
Hi, Josh-
Indeed, the following crashed for me on Mac OS (which you are using):
+ Running "bash test_drive.sh", when "test_drive.sh" looks like:
#!/bin/sh
afni -com 'OPEN_WINDOW A.axialimage' \
FT_epi_r1+orig.HEAD
... run in the Bootcamp dataset: ~/AFNI_data6/FT_analysis/FT/. (Note that on Ubuntu, it worked fine).
However, this worked for me, with the
by
ptaylor
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AFNI Message Board
Hi, Renat-
Just to check, is it a problem to install Xvfb? Indeed, having the QC images is immensely useful.
What is the output of:
afni_system_check.py -check_all
on your system?
--pt
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ptaylor
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AFNI Message Board
OHBM? Chaotic? Suuuurely not... Well maybe just due to us being here.
Re. the link---Aaaaah, now I see the issue. The initial link you posted just appears to actually be the main AFNI MB page (judging by hovering over it). This more recent one does appear to be something more specific that kinda resolves to something more specific, but then falls back to the main page. Where is it suppose
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ptaylor
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AFNI Message Board
Hi, Dante-
Re. the broken link---thanks for mentioning, but I think the server was down for a bit. It appears to work now.
Re. #4: what is the output of (yes, include the negative sign):
afni -VAFNI_COMPRESSOR=
Additionally, what does the init_qc_00_overlap_uinp_obase.jpg image that should have been created in the first bit of running the @SSwarper command look like?
--pt
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ptaylor
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AFNI Message Board
Sure, that is a known occurence to happen.
The solution is here:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/auto_image/auto_%40chauffeur_afni.html#troubleshooting
See Issue #1, specifically.
--pt
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ptaylor
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AFNI Message Board
Hi Matt-
The script did work OK for me, that is odd...
This line:
dset_mask = `ls ${dset_t1:gas/.nii/_mask.nii/)`
is just taking the string stored in ${dset_t1}, and replacing ".nii" from it with "_mask.nii", and then searching for that new file name. You can just replace it with the actual dset name, I was aiming to generalize it, but certainly that could be hardw
by
ptaylor
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AFNI Message Board
Hi, Matt-
Are you runnign it as "tcsh"? the :gas/AAA/BBB/ should just be replacing AAA in the string with BBB. By all means, rename the dsets as appropriate.
(I am in Heathrow on way to OHBM, and need to board plane, might not be able to reply to third question quickly...)
--pt
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ptaylor
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AFNI Message Board
Hi, Matt-
(Sidenote: "Paul", please, instead of "Dr. Taylor".)
3dresample can be used to adjust lots of dataset and header properties together---it assumes that things are correct to start with (in contrast to 3drefit, which is used to fix/change just header info, leaving the data unchanged).
You can resample to a new grid, yes, that is typically something that 3dres
by
ptaylor
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AFNI Message Board
Hi, Matthew-
You should be able to use those other dsets. NB: I am not sure what FMRIprep's dset is *exactly*---you could use AFNI's 3dDiff to difference it with the MNI volume you cited.
The pair of FATCAT reference volumes (one pair for T1w, and one pair for T2w) are just: a template, and weightmask (with the weighting being an ellipsoid/spheroid in the subcortical region).
by
ptaylor
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AFNI Message Board
Hi-
The path stuff still needs to be sorted in setup, but have you seen the @chauffeur_afni functionality here:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/auto_image/main_toc.html
... and more specifically here:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/auto_image/auto_%40chauffeur_afni.html
?
That would seem to be doing a looot of what you want, and perhaps
by
ptaylor
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AFNI Message Board
Hi, Dante-
I actually started writing functionality for this back in August, 2021, but then got sidetracked by other things. So, it is not impossible, it is just that the past month + looming OHBM make things a bit difficult to schedule immediately. I will revisit this, though.
--pt
by
ptaylor
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AFNI Message Board
Howdy-
A sidenote-level comment here:
As of Jan 20, 2022 (and I think >=AFNI_22.0.04), there the APQC HTML's vstat block should contain up to 5 statistic/stimuli images. Thus, if you are "only" seeing full F-stat, I suspect that with a more modern AFNI, you would see several Coef+stat images in the vstat block---this might help provide more information. E.g., if the visual
by
ptaylor
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AFNI Message Board
And after further investigation, the culprit for this woe was having spaces in directories on the computer system, which caused some woe in some shell scripts that contained things like:
set here = $PWD
... and later used the "${here}" quantity/string.
Several/most (maaaaybe all?) scripts have been updated to avoid this behavior, wrapping variables in "quotes". It would
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ptaylor
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AFNI Message Board
Hi, Philipp-
I saw it, but it has been an extraordinarily busy week.
I will reply to your email now.
--pt
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ptaylor
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AFNI Message Board
Hi, Osman-
To me, this looks like a reasonable single-subject seedbased-correlation pattern for a PCC-placed seed (default mode network), with standard resting state data.
The QC HTML there will show piece-by-piece useful aspects of processing to verify--e.g., the alignment images just preceding the vstat--so check everything make sure that all is well (or at least that there aren't gl
by
ptaylor
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AFNI Message Board
Hi, Philipp-
To do bandpassing within a ceratin range of Hz, indeed you need to convert the "digital" frequencies to those of physical units (Hz), and indeed this depends on the sampling rate, TR, and number of time points, N. Let's stick with even N for the moment.
The upper frequency (Nyquist) is determined just by TR:
Fmax = Fnyquist = 1/(2*TR).
The spacing of the f
by
ptaylor
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AFNI Message Board
Philipp-
For your power-slope estimate, you would only use the positive half of the spectrum, anyways, and likely not include the k=0 (baseline) wave number. This is due to the nature of the Fourier spectrum coefficients for real input time series: they have a mirror symmetry around 0. That is why most FFT-based outputs are just comprised of essentially the k=0...N/2-1 wavenumbers, and not
by
ptaylor
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AFNI Message Board
Hi, Philipp-
This reply talks about AFNI's 3dPeriodogram, and scipy's scipy.signal.periodogram(); I refer to the latter here as sps.periodogram().
So, neither of the programs involve logs---that is not an issue here (you can take log after).
You can taper approx. similarly in each program---in my example, I will not taper, for simplicity. Therefore, 3dPeriodogram divides the
by
ptaylor
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AFNI Message Board
Hi, Philipp-
I admit I got a bit lost in the description about what the actual question was. Can you please rephrase it directly?
If you are wondering about a factor of 2 difference in a log-plot-based comparison, then I suspect one "power" method is actually calculating magnitude---that is, power is (magnitude)^2, and when you take the log of that, the 2 comes down on the leftha
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ptaylor
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AFNI Message Board
Hi, Lena-
To add to Daniel's comment: would you be able to post your afni_proc.py command here? We might have some suggestions for that.
And also, as Daniel noted, for human data we lean on @SSwarper now pretty strongly for both skullstripping and nonlinear registration (in humans; for animal data, we would use @animal_warper---but I assume you are looking at human data at the momen
by
ptaylor
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AFNI Message Board
Hi, Osman-
That is a good thing to check. There is even an automatically generated image of seedbased correlation for the DMN in the afni_proc.py generated QC HTML. From your output/results directory, copy+paste:
afni_open -aw QC_*/index.html
... and jump to the "vstat" section. How does that look?
The BOLD effect can be observed outside the brain (meaning here, the final an
by
ptaylor
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AFNI Message Board
Hi, Philipp-
With this kind of resting state-like processing, the regression model is basically full of regressors of no interest. The "output" signal for further use is then the leftover residuals. From your applied case, it seems like the question is: is the quality of fitting in the first 400 time points different than that of the remaining ones, such that the residuals would h
by
ptaylor
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AFNI Message Board