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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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Results 31 - 53 of 53
Good Morning!
Curious if there was any resolution to this issue? Thanks!
Edwin
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ebaldelo
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AFNI Message Board
Thank you for looking into it :) Yes, that confused me as well. It seems to be able to successfully toggle the function (the word 'Fading' will appear and disappear) but nothing else happens in the graph window. Thank you!
Edwin
by
ebaldelo
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AFNI Message Board
Thank you very much for your prompt response. Yes, I have tried that and it doesn't engage a gray background in the graph window as I desire. I've attached another screen shot that I took a while ago of what I'm trying to re-create. Maybe I'm targeting the wrong function to enable this. Any insight into how to do this would be greatly appreciated.
Thank you,
Edwin
by
ebaldelo
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AFNI Message Board
Hi All,
A while ago, I used to be able to perform threshold fading; i.e. through overlay and thresholding, I could see in the graph window some boxes as white and others as gray. For the life of me, I can no longer figure out how to do this. Below are my attempts to resolve this:
(0) Updated afni. (output from >afni -ver:
Precompiled binary macos_10.12_local: Aug 4 2020 (Version A
by
ebaldelo
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AFNI Message Board
Hi PT,
Thank you so much for the response. Works great!
Cheers,
Edwin
by
ebaldelo
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AFNI Message Board
Hi All,
I'm fitting some data and I've gotten an error I have never seen before. At the end it outputs this:
...
++ Job #0 waiting for children to finish; elapsed time=1519.444
++ Job #11 finished; elapsed time=1529.859
++ Job #10 finished; elapsed time=1539.816
++ Job #1 finished; elapsed time=1539.950
++ Job #9 finished; elapsed time=1553.419
++ Job #8 finished; elapsed ti
by
ebaldelo
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AFNI Message Board
Hi All,
I have another seemingly simple questions. For an existing BRIK, how would I go about changing the voxel dimensions? Curious in general but most interested in how do I change the associated time stamp in a 3D+t data set. I've read through '3dTcat' and saw it allows to change 'TR'. Is that a way to set a timestamp between 3D datasets?
Thank you all!
Cheer
by
ebaldelo
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AFNI Message Board
Hi All,
Apologies in advance for the simple question:
Sometimes I am able to see which voxels are masked (white background) and which voxels are not in my mask (gray background). I can't seem to figure out why sometimes it works and sometimes (now) I can not get the mask I have created to do this operation in the AFNI graph vieer. I created my mask in matlab, saved as nifti, and then
by
ebaldelo
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AFNI Message Board
Hi PT/All,
After reading into the documents of different functions it seems like '3drotate' is just what I need. I think I initially overlooked it because I presumed it was just pure rotation and didn't realize you can also translate with it. I will try it out. Thanks for your time!
Cheers,
Edwin
by
ebaldelo
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AFNI Message Board
Hi PT,
Thank you for your response and time into this issue. In response:
1. Yes, both are time series (3D + t, or 4D). '3dinfo -nv' yields 8 and 13, respectively.
2. Yes, just motion (translation + rotation). Not aiming to consider distortions or any non-rigid transformations at the moment. (I think you consider translation or motion as both rigid, but new to registering so p
by
ebaldelo
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AFNI Message Board
Hi All,
I have two sequential data sets I want to compare. So I'd like to do some inter and intra registrations. The first is T2-weighted (DATA1), and the second is T1-weighted (DATA2), so different contrast. I am trying to work on the registration and I think I've progressed decently but there's one part I would appreciate some guidance on, please.
I've registered the f
by
ebaldelo
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AFNI Message Board
Hi All,
From previous searches I understand this might be a bit of exasperating topic, so I apologize in advance. But I just got a new computer and attempting to install AFNI on it and the plugins available after installation appear to be incomplete compared to my previous installation of it. To give you some background;
1. It appears I am using the following version:
Version AFNI_19.2.01
by
ebaldelo
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AFNI Message Board
Hi Daniel,
Thank you for the clarification and response. If I may explain my situation a bit further, I think it might help to clarify what I mean by merge. So the two data sets I have are time points 1 and time points 2. After I have reoriented the 2nd data set in reference to the other (with the adjusted 3dWarp as you suggested), how would I go about to adding them in succession to a new 3d+
by
ebaldelo
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AFNI Message Board
Hello All,
I thought this issue would be straight forward but I seemed to have run into some issues. I ultimately have two 3d data sets that I want to merge using 'to3d'. They are nifti file formats and, verified with '3dinfo', one is oblique and the other isn't. They both are the same matrix sizes. I'd like register the oblique data set to the cardinal, or non-ob
by
ebaldelo
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AFNI Message Board
Ah, figured it out:
3dCalc \
-a 'filename+orig' \
-dsWRAP \
-b 'a[0,-6,0,0]' \
-expr '(b)' \
-prefix savefilename
where means translation in any of the directions and '-dsWRAP' is to wrap around. More info can be found in the manual for 3dCalc.
by
ebaldelo
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AFNI Message Board
Hi All,
I have a simple question. Is there a way to do a circular shift/permutation. I've tried using '3drotate' and just doing a bshift. But it seems to just shift the data whichever direction and replacing it with a new, seemingly random, number column or row. Thanks always for the assistance.
Cheers
by
ebaldelo
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AFNI Message Board
Thank you so much! I really appreciate it. Hah, that's right!
by
ebaldelo
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AFNI Message Board
Hi,
Thank you for the clarification. The adaptive mean function does a nice job of smoothing data, better than the linear smoothing that 3dTSmooth uses. Does one have the ability to save the data from 'Trans 1D' into a BRIK? I'd like to smooth the data and then test different fits on the smoothed data out of curiosity to how the fits will change. So my ultimate goal would be abl
by
ebaldelo
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AFNI Message Board
Hi All,
I've been trying to figure out how to reproduce a function from the '1D Trans' Plugin. I want to replicate the function 'adptMean9' but from the command line so I can save it into a new BRIK. It seems to be a type of smoothing filter for 3D+t data but I don't see that as a default option in '3dTSmooth'. I assume it takes the 9 data points and cal
by
ebaldelo
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AFNI Message Board
Hi all,
I appreciate the previous elucidation on AFNI. My next inquiry comes from the difference in plugin vs. script function. I've been able to fit my data with the script function:
>>3dNLfim -input TimeSeries4+orig.BRIK -signal DiffExp -noise Linear -bucket 0 regressionfitDiffExp
and it comes out fine as a bucket with all the expected parameters. But when I try to do this v
by
ebaldelo
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AFNI Message Board
Ah. I got it working. Thank you. I have another question on the 3dNLfim function now but I will start a new thread for it. Thank you!
Cheers
by
ebaldelo
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AFNI Message Board
Hi all,
I'm a relatively new AFNI user. I've gone through the "Suggested reading for beginners" first to thwart posting redundant inquiries but I have come across one that seems to elude me. I've fit some dynamic data using the 3dNLfim function and I'm trying to pull it up with current dataset. According to the paper on 3dNLfim by Ward, It talks about using a
by
ebaldelo
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AFNI Message Board
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