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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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Dear AFNI community,
We have been developing an open-source parallel processing software package for fMRI analysis (that we have named BROCCOLI) and we are finalizing a manuscript comparing our algorithms with other open-source packages (SPM, FSL, AFNI). The goal is not to have “winners,” but to highlight the advantages and limitations of parallel CPU and GPU-based processing. Since BROCCOLI
by
andek
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AFNI Message Board
I want to apply 3dretroicor to my data and wonder if it should be applied before or after slice timing correction?
The help states
"This program uses slice timing information embedded in the dataset to estimate the proper cardiac/respiratory phase for
each slice. It makes sense to run this program before any program that may destroy the slice timings (e.g. 3dvolreg for
motion correct
by
andek
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AFNI Message Board
Yes it even works for a 4D file, is it also possible to get the output to a textfile?
by
andek
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AFNI Message Board
Is there any AFNI function that gives the mutual information between two volumes, or between one volume and a 4D dataset?
by
andek
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AFNI Message Board
3dBrickStat -absolute -sum gives me an error...
** ERROR: Error - unknown option -absolute
by
andek
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AFNI Message Board
Thanks,
if I use the TT27 as a mask, my cluster should be about 3700 voxels to be significant. With a subject mask, the result is about 150 voxels. Which threshold should I apply if I look at the data in Talairach space (TT27 as underlay), 3700 voxels?
by
andek
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AFNI Message Board
I have made a second level analysis through uber_ttest.py and would like to estimate the significance of a cluster.
-fwhm s, is this in mm FWHM?
The amount of smoothing, can I use the estimated blur from a single subject?
blur estimates : 6.50091 6.22995 6.48386
e.g. use -fwhm 6.5 ?
3dFWHMx says that a stats image should NOT be used, but the folder for the group results
by
andek
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AFNI Message Board
I want to compute the sum of squares (or absolute sum) of a single volume (stored as one nifti file) but I can't find any function for it. 3dTstat does it for each voxel time series.
by
andek
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AFNI Message Board
Sorry, I had misunderstood the meaning of fixed effect for fMRI.
by
andek
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AFNI Message Board
For group analysis, is 3dttest++ equivalent to a fixed effect model and 3dMEMA equivalent to random effect model?
by
andek
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AFNI Message Board
If there is a uber_ttest.py, why is there no uber_anova.py ?
by
andek
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AFNI Message Board
Why is it not possible to simultaneously select underlay and overlay? If I have a list of files open for underlay and click on overlay, underlay closes and vice versa. This makes it cumbersome to for example look at registration overlap for different subjects. I know that I can solve it with scripts, but I would like to do it in the GUI as well.
by
andek
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AFNI Message Board
Is it possible to get a quiet 3dmerge output? I don't want to see "Editing sub-brick 142" and so on.
by
andek
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AFNI Message Board
Hi,
I have a question about uber_subject.py. Under "extra regress options" I can choose "regress motion derivatives". Does this refer to the estimated motion parameters or their time derivatives? If I don't check the box, is regression with the "ordinary" motion parameters (i.e. not derivatives) still performed?
Anders
by
andek
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AFNI Message Board