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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
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Thanks for the help. This is the solution I came up with too, but was hoping there was a more automated way of finding the first and last indices for the condition.
And yes, I used 'stim_times_IM'
by
donnajb
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AFNI Message Board
Hi,
thanks for the help, but that solution isn't quite right. I'm not trying to include All sub-bricks in the dataset, just all of the sub-bricks that apply to one condition. For example, Cond1 Coefficient values could be alternating sub-bricks between 1-21, and Cond2 Coefficient values could be alternating sub-bricks between 22-56, and so on.
So I'm still looking for some k
by
donnajb
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AFNI Message Board
I used the duration-modulated parameter for 3ddeconvolve (dmblock), so the output for each condition is not a single average Coefficient value, but instead, it is one coefficient value for each trial. For instance, for Subj1, the Cond1 output includes 'Cond1#0_Coef', 'Cond1#1_Coef', 'Cond1#2_Coef'...'Cond1#10_Coef'.
I want to use 3dmaskave to find the av
by
donnajb
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AFNI Message Board
I do run 3dwarp on the structural image and the functional runs in my script. Should I modify this in the script for this person?
Here is the command for the structural image:
3dWarp -deoblique -prefix $output_dir/$subj.mprage $subj.mprage.nii
and for the functional runs:
# tshift
foreach run ( $runs )
3dTshift -tzero 0 -quintic -prefix rm.r$run.tshift pb00.$subj.r$run.tcat+orig
by
donnajb
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AFNI Message Board
Hello,
I am having problems preprocessing one subject. I acquire 6 functional runs and then collect the structural image at the end. This participant needed to come out of the scanner between runs 4 and 5. After putting him back in, it seems that we placed him in the coil slightly differently, because runs 1-4 do not quite line up with runs 5 and 6. Furthermore, the angle of the bounding box w
by
donnajb
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AFNI Message Board