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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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While I wasn't able to get the 'pen' option to work, I did realize that simply pressing the scroll of my mouse did the trick. I hope that helps someone! : )
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Amy Frithsen
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AFNI Message Board
Hello,
I'm trying to draw a sphere ROI using the Draw ROI plugin option. However, I can't seem to draw the actual ROI. I'm using a Mac and I know there are some issues with this, but I also know I've done it before using the 'pen' option. Right now, the 'pen' option is greyed out and thus cannot be used. Anyone know of a way to turn this option on?
Th
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Amy Frithsen
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AFNI Message Board
Thank you for the info. I'm now using 3dTproject (as suggested by Bob Cox) and this implements the regression, censoring, and bandpass filtering all in one step. So I hope I'm good. thanks again!
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Amy Frithsen
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AFNI Message Board
Perfect thank you! I REALLY appreciate the quick response. there always seems to be some super convenient AFNI command that I do not know about : )
by
Amy Frithsen
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AFNI Message Board
Hey AFNI folks,
I'm running a resting-state functional connectivity study and am trying to follow the methods outlined in a paper by Power et al. 2014 (doi:10.1016/j.neuroimage.2013.08.048). As a result, I am wanting to do bandpass filtering after regression of nuisance variables (motion, csf, etc.) has been carried out.
I do the regression using 3dDeconvolve and use the -censor fla
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Amy Frithsen
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AFNI Message Board
Hi AFNI folks,
I'm trying to run 3dDeconvolve using the motion parameters (from align_epi_anat.py) and their derivatives as regressors. First I detrended the motion parameters and then got their derivatives using 1d_tool.py. When I pass these on as regressors in 3dDeconvolve, I get warnings that my regressors are (nearly?) collinear. This makes sense since they are simply derivatives of
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Amy Frithsen
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AFNI Message Board
Thanks. I had looked into this, but realized that it will estimate the mode at each volume, where what I really want is one value that is the mode of all voxels across all volumes. But I guess I can do it volume by volume and then compute overall. I just figured there might be a more straightforward way of doing this. But thank you!
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Amy Frithsen
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AFNI Message Board
Hey AFNI folks,
I'm trying to determine the mode of all voxels across the entire brain throughout time (within each functional run). Is there a straightforward way to do this? I want something like 3dBrickStat, but don't see an option for mode available.
Thanks for any help!
~ Amy
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Amy Frithsen
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AFNI Message Board
3dcalc - 8 years ago
Hello,
I'm trying to mask an image with a certain threshold. I understand that I can do this with 3dcalc in the following way:
Example: if I want to use a threshold value of 3, then 3dcalc -a file.nii -expr 'iszero(a-3)' -prefix maskimage
The output will be zeros where values do not equal 3 and 1s where they do
But now I want there to be several threshold values. Fo
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Amy Frithsen
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AFNI Message Board
Hello AFNI world,
I ran ANATICOR on my data and it worked beautifully on most subjects. But for three of them, there was a 'no voxels survive threshold' error. I got around this by using the '-no ventricles' option. I was hoping though to play around with the radius parameter to see if I could tweak that in order to still get some reliable signal from the ventricles for
by
Amy Frithsen
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AFNI Message Board