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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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Hello AFNI gurus, happy new year;
I'm trying to replicate an AFNI routine in MATLAB. We first do a periodogram of an fMRI time series, then smooth it with the following command:
3dTsmooth -hamming 7 periodogrammed_fMRI
I tried to read the documentation of 3dTsmooth and it was a bit unclear to me. Does it applies a hamming window of 7 time points as windows to data. For example, if t
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duodenum
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AFNI Message Board
Thanks. 11 is working fine but just out of curiosity, is there a way I can operationalize example 11b the way I want?
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duodenum
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AFNI Message Board
Just to give an update on this one: the script with recon-all worked perfectly and took only 3-4 hours with 16 threads, which I guess, a reasonable time for a script with recon-all + @SSwarper + afni_proc.py.
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duodenum
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AFNI Message Board
Hi,
There isn't an error message, but the end result is problematic. When I inspect the blocks, problems start from volreg.
I extracted the ventricle mask from this link: . I don't know if it's a reasonable way to do this but kinda followed this thread:
Create ventricle mask in MNI space
For resampling, I picked a previously preprocessed subject's dataset. It was a
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duodenum
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AFNI Message Board
Hi Paul,
Thanks for pointing the -parallel option, I'll try that out today and return back.
On WMe follower datasets, I checked example 11b again but couldn't find anything suggesting a follower dataset. Are you suggesting that I should find something in suma_MNI152_2009 folder?
Thanks,
Yasir
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duodenum
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AFNI Message Board
Just finished running the script and it failed drastically. The problems begin with the volreg block, so probably the mask is problematic. Any ideas why?
Yasir
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duodenum
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AFNI Message Board
Hello dear AFNI gurus,
Following along this question and it's answers: Create ventricle mask in MNI space
I intend to do a resting state analysis without Freesurfer (that takes waaaay tooooo muuuuch time) and want to use MNI152 template. So I'm going through example 11b method (that ventricle extraction method seems okay to me, who am I to judge).
First, I will be running @SSw
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duodenum
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AFNI Message Board
Well, as you said before: Windows: the gift that keeps on giving (headaches)...
This line of code seems to be the problem:
export DISPLAY="$(/sbin/ip route | awk '/default/ { print $3 }'):0"
I have to run it every time I open the terminal (just like XServer).
Is there a way to make it global(ish) so that I don't have to copy paste it every time?
Thanks
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duodenum
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AFNI Message Board
Okay, after trying random stuff advised on message boards, I've figured it out. It works now. Sorry if I caused any inconvenience.
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duodenum
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AFNI Message Board
Hi,
After installation, when I start AFNI on WSL2 (Ubuntu 20.04), it gives me the following error:
Initializing X11 Error: Can't open display: 0.0
++AFNI is detached from terminal
I've launched VcXsrv before starting terminal and I've tried switching to WSL1 too (as advised in other threads).
The output of afni_system_check.py -check_all is following:
root@DESK
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duodenum
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AFNI Message Board
I see. I am using errts files for processing (not doing GLTs) and did the @SSwarper first, so I feed those files to afni_proc. The issue is there are too many subjects and too many runs so using a different afni_proc.py for every run of every subject would mean too much work. If I can't find a way around though, I will use that method.
2^8 is, not important at this point but, suppose you
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duodenum
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AFNI Message Board
Hello dear gurus,
I am doing an analysis with 8 runs (rest, task1, task2 etc...) and when I use afni_proc.py, it concatenates all the runs into one errts dataset. However, I need them independently for my further analyses. I can use 3dbucket to seperate them but subjects differ in respect to tasks (some subjects have all the tasks, some of them only did resting state, some of them did 4 tasks
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duodenum
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AFNI Message Board
Hi Paul,
Thanks for the reply. The paper you send about LZC is very interesting. And ALFF is very interesting too. I discarded the idea of fSD for now because it would take waaaaay too much statistical stuff with all the other measures and states I have but I definitely want to operationalize this in the future. Until then, best of luck, I will go back to lurking in the shadows again.
Yasi
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duodenum
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AFNI Message Board
Hi Paul,
LZC: It looks complicated on paper but it's actually simple and fun when you get the hold of it. Suppose you have this time series:
0.5, 0.1, 0.1, 0.4, 0.5, 0.9, 5, 0.23, 999
First, you take the median of it (for thresholding)
0.1, 0.1, 0.23, 0.4, 0.5, 0.5, 0.9, 5, 999
The median is 0.5.
Second, we round the values to make them a binary sequence (binary in this case
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duodenum
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AFNI Message Board
Hi Paul, thanks for detailed and fast response;
I didn't use censoring, only despiking. I don't know how to deal with censored time points (ple isn't the only measure, I will be doing lempel-ziv complexity, fractional standart deviation etc...) so I tried to be picky about the subjects with as little motion as possible.
As an extension of that, can we generalize your answer?
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duodenum
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AFNI Message Board
Oh, I guess I understood your answer wrong. What I'm doing is:
- Calculate PLE of rest
- Calculate PLE of task
- Compare those
Can we generalize an answer to this issue, as in not only PLE but for every measurement between resting and task data.
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duodenum
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AFNI Message Board
Yes. To be precise:
- Take the power spectrum of fMRI signal (FFT ==> 3dPeriodogram)
- Smooth it with a Hamming window of 15/11/7 (not sure which one to use yet)
- Plot it with their respective frequencies
- Take logarithms of power spectrum and the frequencies to make it more linear-ish
- Fit a linear regression line to the logarithms
- The slope of that line is power-law exponent.
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duodenum
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AFNI Message Board
This might be a somewhat amateurish question. I have resting state and task datasets of some subjects and I want to compare these two for a rest vs task analysis of their power-law exponents. TR=2 s for both. But the resting state data has 148 time points and task has 330 (110 time points for each of the 3 runs). Can I compare those two (148 vs 330 time points) or should I select 148 time points
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duodenum
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AFNI Message Board
Okay I think I understood the problem. Somehow I marked right anatomical datasets but gave the same epi dataset to all subjects when setting up afni_proc.py. I couldn't delete my initial post though.
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duodenum
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AFNI Message Board
Hello dear AFNI gurus;
After I batch preprocessed my data (usual for subj in bla-bla) using afni_proc.py and running the scripts generated by it, I realized an unusual problem. When I looked at the QC files, the information about motion was same across ALL subjects.
Quotemotion limit : 0.3
num TRs above mot limit : 7
average motion (per TR) : 0.103047
max motion displac
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duodenum
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AFNI Message Board
Hello AFNI gurus and fellow AFNI n00bs;
When I use 3dfim+, it gives this message:
This program (3dfim+) is very old, may not be useful, and will not be maintained.
But I couldn't find which program I should use instead. Do you have any recommendations?
Thanks,
duodenum
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duodenum
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AFNI Message Board