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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
Page 3 of 3
Pages: 123
Results 61 - 74 of 74
hi all
I am trying to get the alpha feature to work, but have not had any luck. I have uploaded a screenshot in jpg format but it does not seem to be attaching.
Anyway, I have turned on the Alpha option to linear, set the floor to 0.2 and set AFNI_EDGIZE_OVERLAY to YES but there is no opacity gradient--instead, all that happens is that I get orange and blue outlines around contiguous supra
by
jkeidel
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AFNI Message Board
hi all
just bumping this up as I noticed that Zhark had not been posting but is now back...
all hail almighty Zhark
James
by
jkeidel
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AFNI Message Board
Hi everyone
Has any further progress been reported on this? We are very keen to introduce some sort of distortion correction into the analysis pipeline for the studies we are about to run and of course staying within AFNI would be ideal. Otherwise, could someone give a reference for the blip-left and blip-right method of computing the distortion field for gradient echo EPI? I know the Emble
by
jkeidel
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AFNI Message Board
hi all (especially Bob, the Mad Correlator I suppose)
I was wondering if it would require great efforts to add an option to 3dGroupInCorr to allow the seed vectors to come from a separate dataset, as is possible using the ExtraSet option in interactive InstaCorr. I would like this feature so that I can do seed-based correlations from independent datasets. I understand that I can use the VECT
by
jkeidel
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AFNI Message Board
here's one way that I think should work:
3dcalc -a setA+view'' -b setB+view'' -expr 'a*ispositive(a-b)' -prefix output
hope this helps
James
by
jkeidel
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AFNI Message Board
If you apply ReHo to your residual time series and then run 3dFWHMx then I don't think you are measuring the smoothness of the signal, just the additional smoothness that comes from making the value of any voxel dependent on its neighbors. but maybe I'm missing something?
by
jkeidel
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AFNI Message Board
we have this same problem estimating the smoothness that results from doing searchlight analysis. could you possibly apply ReHo to the residual time series then use 3dFWHMx on the result to estimate the smoothness of your maps?
by
jkeidel
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AFNI Message Board
Daniel-
the coordinates in question are 74L, 6A, 10I and 72L 4A 10I. they really aren't that close to the brain. the reason I am worried is that I would like to say whether my findings do or do not square with the reported ones but that is pretty hard when we are talking about empty space. I understand your point about blurring, though I am surprised to see the peak voxel so far out.
by
jkeidel
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AFNI Message Board
hi all
I am looking at some coordinates reported in a paper which used AFNI and registered data to the MNI_EPI template. they are in the STS. I am used to talairach space, and am a bit confused. basically, a number of the peak coordinates for ROIs in transformed individual brains given are > 70 mm L/R, and when I put the crosshairs of the viewer on some of the reported coordinates they a
by
jkeidel
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AFNI Message Board
hi all
I am interested in running some laterality analyses and am trying to make a symmetric template (in spite of the hemispheres of real brains not being so...). So I split the TT_N27 brain in half then changed orientation to LAI from RAI. However, because they are in different orientations I can't just add them back together--it looks good in the viewer window if I make one the overl
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jkeidel
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AFNI Message Board
Right-click on DataDir in the controller window...
best
James
by
jkeidel
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AFNI Message Board
if Gang's suggestion doesn't work, you could try something like:
#!/bin/tcsh
set runs = yourNumberOfRuns
foreach f (`ls *1D`)
set c = 1
set stem = `echo $f | sed s/.1D//`
cat $f | head -$c | tail -1 > $stem.r0${c}.1D
@ c = $c + 1
end
end
I know it's not what you are looking for but I had had do this myself when I wanted to do an analysis of each run
by
jkeidel
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AFNI Message Board
hi Shant
I think the problem here is that it is unlikely that the measure you want (which might be given by using 3dmean on the R-squared subbrik) would really be all that useful. it doesn't really make sense to me at least, because you will be averaging together a bunch of values only some of which are meaningful--for instance, if you are dealing with task-based functional data then the
by
jkeidel
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AFNI Message Board
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Pages: 123