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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 4 of 5
Pages: 12345
Results 91 - 120 of 145
Hi everybody,
Following Gang's instructions, I've run some PPI analysis. I created my PPI regressors for two stimuli types F, and S coded as 1 and -1 respectively in the interaction regressor. Thereafter I run 3dDeconvolve with the interaction regressor (after wavering). I then extract the R^2 and convert appropriately to z-scores. Since I have two groups, N and M, I then subject the
by
Colm Connolly
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AFNI Message Board
Hi Rick,
rick reynolds Wrote:
-------------------------------------------------------
> Colm, if I were to add such a model function:
> a. Would this satisfy your needs?
> b. Would you want to fit all 7 parameters, or is
> there a reasonable subset that would work?
I'd definitely try to use it.
My previous attempts at fitting the gamma model using R worked but
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Colm Connolly
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AFNI Message Board
Hi everybody,
I wonder does anybody know of a hemodynamic model that incorporates an initial dip? I've been using
fval = gs[1] * exp( log(t-gs[0]) * gs[2] ) * exp(-(t-gs[0])/gs[3]);
from model_gammavar.c translated into R, but unsurprisingly it's not capturing the initial dip and is rather setting a delay instead.
Thanks,
Colm.
by
Colm Connolly
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AFNI Message Board
Hey,
You could add -DAFNI_FLOATIZE=YES to the beginning of your 3dANOVA2 command to make it save the output as floats instead of shorts. This should make these warnings disappear. There is a more detailed message about this at the bottom of the help message printed to the screen by 3dANOVA2 if you run it without command line arguments.
Bye,
Colm.
by
Colm Connolly
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AFNI Message Board
Do you have a ~/.bash_profile as well as ~/.profile? If so bash will preferentially read the former and ignore the latter. This could be the source of your problem. Have you tried opening ~/.profile in an text editor to ensure that the lines to add afni to the path are actually in ~/.profile?
Also I notice that you commands above refer to .profile. Were you in ~/ when you executed these comman
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Colm Connolly
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AFNI Message Board
yep sure can, I don't need the new bells and whistles in R 3.0.0.
I'd still have a look at line 23 in AFNIio.R since it returns true regardless of whether the R_io.so loads successfully or not.
For example consider the following:
R version 2.15.3 (2013-03-01) -- "Security Blanket"
Copyright (C) 2013 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platfo
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Colm Connolly
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AFNI Message Board
Nope I was 64-bit all the way. I just downloaded AFNI again and installed it along with the 64-bit version of R 3.0.0. The result of the combination of these two is the following:
R version 3.0.0 (2013-04-03) -- "Masked Marvel"
Copyright (C) 2013 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin10.8.0 (64-bit)
R is free software and comes with ABSOLUTELY
by
Colm Connolly
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AFNI Message Board
Hi Thomas,
Using FAST to segment T1s is relatively straight forward and considerably faster than Freesurfer especially if you do not need all the other bells and whistles that Freesurfer gives you.
fast -t 1 -g -p -o segment ${subjectNumber}.anat_struc_brain.std.nii.gz
will segment your T1 into grey, white and csf.
AFNI also has 3dSeg which segments T1s. You might try that as well. I
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Colm Connolly
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AFNI Message Board
Hi Gang,
It appears that R_io.so was built under R 2.14 and will not load on R 2.15.3 which I'm running. While trying to figure out why read.AFNI was printing the following and terminating on me
** Error:
Missing R_io.so
I found a a problem in AFNiio.R at line 23 in the set_R_io definition
Currently it reads
if (!exists('dd')) {
but should read
if (inherits (dd,
by
Colm Connolly
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AFNI Message Board
Hi,
Can anyone tell me please what version fo R is AFNI built against?
I currently have the following installed:
Version AFNI_2011_12_21_1014
[[Precompiled binary macosx_10.6_Intel_64: Apr 26 2013
Thanks,
Colm.
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Colm Connolly
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AFNI Message Board
you could try something like this:
Xvfb :1 -screen 0 800x800x24 &
# saves the PID of the Xvfb process so we can kill it when we're doen with afni
x11DisplayPID=$!
x11DisplayArgument="-display :1.0"
## then you can run afni like this
## replace $otherCommandsGoHere with the other commands you want afni to run
afni $x11DisplayArgument $otherCommandsGoHere
if
by
Colm Connolly
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AFNI Message Board
Hi Jon,
3dPAR2AFNI.pl will do the conversion for you.
Bye,
Colm.
by
Colm Connolly
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AFNI Message Board
Hi Mika
You likely need to use a 64 bit version of AFNI to load this file, which at 4.3 bytes is over the addressable memory range of a 32 bit binary.
Bye,
Colm.
by
Colm Connolly
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AFNI Message Board
Someone in the office told me about the Dice metric a few minutes after I poster my original query. I should have figured that AFNI would have more than one way to do this Thanks for all the suggestions.
by
Colm Connolly
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AFNI Message Board
Hi,
I have two cluster maps derived from some rs-fMRI. Now I'd like to determine the similarity of two cluster maps. I could do a simple subtraction but that would leave me with zeros in the voxels common to both cluster maps. Can any one recommend a metric that can quantify the concordance of the two cluster maps?
Thanks,
Colm.
by
Colm Connolly
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AFNI Message Board
Hi everybody,
When Pos? is unselected and autoRange is also unselected, does the number entered in the "OLay value that maps to 1.0 for the color overlay" field also map to -1.0? For example if I enter 2.5 to map to 1.0 on the color overlay does -2.5 map to the -1.0 on the color overlay?
Secondly, how do I make an image of the color map? I'd like to make an image of Spectrum:
by
Colm Connolly
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AFNI Message Board
Hi Daniel,
It's not the number of notes that's giving me problems. its the max length of an individual note. For example, I'm trying to add some notes to the header to indicate what subjects went into an LME. The attached R code seems write, but when I run 3dinfo on the file after note has been added, the note is truncated. In addition to inserting a note indicating what subject
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Colm Connolly
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AFNI Message Board
Hi,
Does afni have a limit on how big a note in the header can be? If so what is it?
Thanks,
Colm.
by
Colm Connolly
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AFNI Message Board
Hi everybody,
I'm trying to update AFNI by downloading the Mac OS X Lion (10.7 Intel) 64bit tarball from
but when I run the afni in the extracted directory it tells me
colmconn@Colms-iMac:/Volumes/opt/software/macosx_10.7_Intel_64> ./afni -ver
Version AFNI_2011_12_21_1014
[]
If I try to use @update.afni.binaries but it tells me
colmconn@Colms-iMac:/Volumes/opt/software/ma
by
Colm Connolly
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AFNI Message Board
I found the best way to get around this is to enlarge the image produced by AFNI using convert from imagemagick
f=imageToEnlarge
convert $f -resize 300% new-$f
mv -f new-$f $f
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Colm Connolly
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AFNI Message Board
Ah, I get you now. I didn't realize that libglib was included in the afni package. Problem solved. Thanks.
by
Colm Connolly
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AFNI Message Board
Thanks for the replies. The macosx_10.7_Intel_64 tarball that I downloaded yesterday still seems to require glib:
./3dSkullStrip
dyld: Library not loaded: /sw/lib/libglib-1.2.0.dylib
Referenced from: /Users/colmconn/macosx_10.7_Intel_64/./3dSkullStrip
Reason: image not found
Trace/BPT trap: 5
Is this a build mistake?
How about depending on macports rather than fink? It seems t
by
Colm Connolly
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AFNI Message Board
Hi everybody,
I'm trying to install AFNI the way recommended here
since there do not seem to be specific instructions for Mountain Lion (I've read this thread but it doesn't solve the glib problem.)
While I got AFNI up and running, I've run into problems with fink and the apparent lack of a glib package suitable for use with macosx_10.7_Intel_64.tar.gz that I've
by
Colm Connolly
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AFNI Message Board
Hi Rick.
Combining the bandpass filtering and motion correction has led me to through out 19 subjects from my analysis, which is unfortunate. I have used 0.2 for the threshold on the Euclidean norm, plus my subjects are adolescents.
Can you tell me how does combining the two make the impact on the DoF explicit? That's the part I'm not so clear on.
Thanks,
Colm.
by
Colm Connolly
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AFNI Message Board
Hi everybody,
I'm (re)writing the methods section of a resting state paper where the analysis is based on example 9 in afni_proc.py. I just want to include a couple of lines on why including bandpass regressors in the model matrix has advantages.
Those that I can come up with include:
1. permits censoring without having to break the time axis or replace censored time points with inap
by
Colm Connolly
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AFNI Message Board
If you're doing whole brain correlation and correlating the average from a seed region with the whole brain, you should observe almost perfect correlation between the seed timeseries and the region in the brain from which the seed timeseries was extracted.
Do the correlations make sense based on your groups and hypotheses?
The absence of negative correlations may be due to the absence
by
Colm Connolly
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AFNI Message Board
didi you log out and back in after you installed xquartz?
by
Colm Connolly
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AFNI Message Board
You could just do this with 3dfim+. It seems to me to be the most straightforward way of doing it.
3dROIstats -quiet -mask_f2short -mask ${seed} mytimeseries+tlrc.HEAD > ${seedTimeseriesDir}/${seedName}.1D
3dfim+ -input mytimeseries+tlrc.HEAD -ideal_file ${seedTimeseriesDir}/${seedName}.1D -out Correlation -bucket ${rsfcDir}/${seedName}_corr
and just for good measure Fisher Z transfor
by
Colm Connolly
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AFNI Message Board
Are you censoring a lot of your data? So much so that there are too few time points left to run the analysis?
by
Colm Connolly
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AFNI Message Board
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Pages: 12345