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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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Hi Rick,
Thank you for your help. Using 3dcalc was a bit cumbersome as the number of reference waveforms can vary and is often a large number
I also needed to extract the associated beta value.
I found another way that I think works using 3dTstat. Also, would you use the full R^2 or Stim#1 R^2 ?
Here is what i wrote:
foreach n (`seq -f %02g 0 $n_max`)
3dDeconvolve -mask ${mask}+orig -
by
julienjulien
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AFNI Message Board
3dfim+ - 1 year ago
Hi all,
I have been using 3dfim+ for a long time because I need the "Best Index" option.
3dfim+ -input CVR_raw_scaled+orig -ideal_file pco2_multi.1D -polort 1 -out 'Fit Coef' -out 'Correlation' -out '% Change' -out 'Best Index' -bucket CVR_slope
I know it is very old but I could not find the equivalent option using 3dDeconvolve.
3dDeconvolve
by
julienjulien
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AFNI Message Board
I have just read your doc. It helps a lot and clarifies the use of -stim_times_AM1.
Thank you very much to write that in such a short time!
I will try it on our data in a week or 2 ...
Julien.
by
julienjulien
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AFNI Message Board
Thank you so much!!
I did not open the link yet but I'll let you know after I try.
by
julienjulien
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AFNI Message Board
Hi Robert W. Cox,
"If the above is the case, then I figured out how to do this with 3dDeconvolve, combining the -stim_times_AM1 option and the TENT(b,c,n) response model. Although I wrote this code, I never thought of using it this way. "
Thank you, so I should be able to do it with those 2 options, right? I looked at -stim_times_AM1 and see how it could works ... but will have
by
julienjulien
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AFNI Message Board
Thank you very much for your reply.
Yes, it is exactly what I want to do :)
by
julienjulien
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AFNI Message Board
Hello AFNI group,
I have already posted the message below but did not get an answer yet, so I try to re-post ... sorry about that.
I am working with brain vascular reactivity data (CVR) and analyze our data using AFNI.
We use changes in CO2 as our stimulus file and acquire data using BOLD imaging.
We usually do a simple linear regression of BOLD by the end tidal CO2. (3dDeconvolve -mask
by
julienjulien
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AFNI Message Board
Hello AFNI group,
I am working with brain vascular reactivity data.
We use changes in CO2 as our stimulus file and acquire data using BOLD imaging.
We usually do a simple linear regression of BOLD by the end tidal CO2. We also have a script to convolve the the end tidal CO2 with an exponential of variable time characteristic to account for variable speed of vascular reactivity depending on
by
julienjulien
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AFNI Message Board
Hi Taylor,
@chauffeur seems to be way more user friendly, although I already had all my scripts using afni -com ...
Also, I don't think afni -com ... had the option to use a label in the image. I will try that.
In term of concatenation images, yes indeed I was already using imcat, which is nice.
To the issue of not displaying an overlay if it does not exist: I understand that I c
by
julienjulien
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AFNI Message Board
Hi Rick,
Thank you about that... Otherwise I can still use the account I am using now (julienjulien)
Thanks
Julien
by
julienjulien
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AFNI Message Board
Thanks so much.
I will try that that. I did not know anything about @chauffeur
by
julienjulien
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AFNI Message Board
Hi,
I am using the AFNI "driver" (afni -com ... ) capability to create a lot of maps on a weekly basis.
I wanted to ask for a long time if it was possible to add a variable or environment variable to tell afni to NOT save any image (-com 'SAVE_JPEG A.axialimage imA' ) when the corresponding afni file does not exist.
Currently, if the overlay does not exist, it will display
by
julienjulien
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AFNI Message Board
Hi,
I had to create a new account because I could not retrieve my password.
Indeed, the "send password" button never send a password to my email address. I tried many times.
Do you know why?
Thank you.
Julien.
by
julienjulien
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AFNI Message Board