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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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Results 1 - 11 of 11
Questions
1) Given an event ("mem") repeated in each run, can the following be interpreted as the same:
a) modeling all events across runs using a single -stim_times ( -stim_file "all_runs.1D" -stim_label "mem")
b) modeling each run separately (-stime_label "mem_run1" ... -stim_label "mem_run2") and combining with gltsym ("gltsym:mem_run
by
Will Foran
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AFNI Message Board
you'll need administrator privileges to install packages. the easiest way (if it's setup) is
sudo apt install libudunits2-dev
you could also try using the root user, if you have the password
su -c "apt install libudunits2-dev"
by
Will Foran
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AFNI Message Board
Burried in the output is a hint
QuoterPkgsInstall
Configuration failed because libudunits2.so was not found. Try installing:
* deb: libudunits2-dev (Debian, Ubuntu, ...)
Maybe try
apt install libudunits2-dev
rPkgsInstall -pkgs ALL
It might take a few tries to identify and get all the dependencies
by
Will Foran
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AFNI Message Board
I imagine there is an easier way to make a mask for a p-value threshold given an f-stat subbrick.
Our strategy is to extract the statpar of the brick and use that with fift_t2p. I think we could also use e.g. stat2cdf(0.05,4,$ab,0) or cdf -p2t fift .005 14 882 | sed 's/t = //'.
Either way it seems like we are tripping over ourselves to extract and feed back data 3dcalc might alr
by
Will Foran
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AFNI Message Board
neurodebian for ubuntu 16.04 doesn't have afni yet.
AFNI gui requires libxp which is also absent from the repos.
Quoteafni
afni: error while loading shared libraries: libXp.so.6: cannot open shared object file: No such file or directory
Fortunately (and surprisingly) building libXp is straight forward.
The code below gets afni running albeit in a bit kludgey way.
# prere
by
Will Foran
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AFNI Message Board
I'm in the same lab, using the same computer as andrew
# R installed from r-project packaged pkg, not fink
» which R
/Library/Frameworks/R.framework/Resources/bin/R
» R --version
R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
Copyright (C) 2013 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin10.8.0 (64-bit)
» afni --version
Version AFNI
by
Will Foran
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AFNI Message Board
Is there an official configuration supported for the newer OS X version?
We have two Mac Pros each now running on OS X 10.9, one with binaries for 10.8 and the other with 10.7 binaries. The 10.8 binaries seemed to require more fiddling. (needed DYDL_LIBRARY_PATH in addition to the fallback environment variable for 3dDespike to find the dydl's needed)
» uname -mrn && afni -ve
by
Will Foran
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AFNI Message Board
We just got this error using a version of R packaged/installed with fink. We changed the environments path so the OS X native install of R was used instead.
in ~/.profile
# use R not from fink
export PATH="/Library/Frameworks/R.framework/Resources/bin:$PATH
by
Will Foran
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AFNI Message Board
Sorry for the long post!
The 4 question below boil into
What is the best way manage MNI coordinates and afni_restproc.py output? (just one line change in the tsch script?!)
Is tlrc's use in AFNI historically motivated? Why TT over MNI?
Thanks!
Will
We're running afni_restproc to emulate the Power Neuroimage 2012 pipeline. We already ran some 300 subjects through res
by
Will Foran
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AFNI Message Board
I ran dcm2nii and Dimon on the same set of dicoms. I'd like to resample the dcm2nii nifti to the Dimon BRIK/HEAD. When I try 3dresample, the bottom of the brain is truncated/clipped off.
Is the field of view different and incomparable?
I stumbled into this pursuit accidentally. But I am curious if this can be done without aligning the (identical) images first.
Thanks!
Will
by
Will Foran
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AFNI Message Board
Hello AFNI gurus,
Is there a nice/readable way to use and <range> selectors to select values thresholded by a different subbrick?
For instance, to get the beta mean of voxels who's p value is <= .05, I'd like to
3dBrickStat -mean values+tlrc'<p:0..0.05>'
but the best way I can think to do this is:
3dBrickStat -mean '3dcalc( -b values+trlc
by
Will Foran
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AFNI Message Board