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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:
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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 2 of 2
Pages: 12
Results 31 - 59 of 59
Hello again,
I've figured out recently how to install missing R packages to make 3dMVM run (I had a post on that here a few weeks ago).
The surprising thing, is that after it already worked and after I tried various models with 3dMVM, it stopped working.
It seems like I have a syntax error, although I am using scripts that have already proven to work.
I thought maybe it has to do wit
by
Galit
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AFNI Message Board
Hi Paul,
This is the command that I used:
3dAllineate -cubic -1Dmatrix_apply S01_ANAT.aligned2epi_mat.aff12.1D -prefix L_Broca_mask1_trans L_Broca_mask1+orig
So, I see now that I need to add a -master variable (as indeed it says in the helpfile, sorry for not noticing that). Then the command should be like this:
3dAllineate -cubic -1Dmatrix_apply S01_ANAT.aligned2epi_mat.aff12.1D \
-m
by
Galit
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AFNI Message Board
Hello AFNI team,
I'd appreciate your help in understanding the dimensions of the aligned output I get from align_epi_anat.py:
I aligned a T1w image to an EPI, using align_epi_anat.py. I used the transformation matrix that I got as output to also align an ROI mask that was defined on the original T1w, so that it would match the EPI (I used 3dAllineate -cubic to do that).
As for the T1:
by
Galit
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AFNI Message Board
Thanks Gang, and everyone! Problem solved - apparently I was missing the xml package, and for that package to compile, I had to run the following code (found it here):
sudo apt install libxml2-dev
After running that, I was able to install phia and afex with no problem.
Thanks again for all the help!
by
Galit
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AFNI Message Board
Thanks Gang. I did as you said, but when I install 'curl' I get the following error:
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because libcurl was not found. Try installing:
* deb: libcurl4-openssl-dev (Debian, Ubuntu, etc)
* rpm: libcurl-devel (Fedora, CentOS, RHEL)
* csw: libcurl_dev (Solaris)
If libcurl is already installed,
by
Galit
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AFNI Message Board
Thanks, unfortunately it still didn't work.
1. In the sources list I changed things as you said (with the actual url and not the hyperlink). Here is the output:
grep -H cran /etc/apt/sources.list
/etc/apt/sources.list:#deb rebecca/
/etc/apt/sources.list:#deb rebecca/
/etc/apt/sources.list:#deb rebecca/
/etc/apt/sources.list:#deb rebecca/
/etc/apt/sources.list:#deb rebecca/
/e
by
Galit
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AFNI Message Board
Thanks. Indeed, I am using Mint.
Running the sudo command did not install the packages, according to the output of afni_system_check.py (I see a warning that afex, phia and brms are not installed).
Running the grep command, I get the following output:
/etc/apt/sources.list:deb rebecca/
/etc/apt/sources.list:deb rebecca/
/etc/apt/sources.list:deb rebecca/
/etc/apt/sources.list:deb
by
Galit
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AFNI Message Board
Hi, here is the output:
-------------------------------- general ---------------------------------
architecture: 64bit ELF
system: Linux
release: 3.13.0-37-generic
version: #64-Ubuntu SMP Mon Sep 22 21:28:38 UTC 2014
distribution: LinuxMint 17.1 rebecca
number of CPUs: 8
apparent login shell: tcsh
shell RC file: .cshr
by
Galit
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AFNI Message Board
Hi,
When I try to run 3dMVM, I get an error that some R packages are missing: phia and afex.
I saw that I wasn't the first with this issue, but I tried solutions that were suggested for other people with the same problem, with no success.
I tried rPkgsInstall -pkgs 'afex', and rPkgsInstall -pkgs 'phia', and I also I tried installing it from R, but I get an error that
by
Galit
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AFNI Message Board
EDIT: Never mind, I found the problem. The file was indeed empty... I was looking at the wrong file. Sorry, and thank you again.
I'm running 3dDeconvolve, and it fails to read the Motion time series file.
The File is not empty and doesn't have weird characters in it (I checked).
Any idea what the problem is?
Here is the script, looping over a few subjects:
foreach i ("
by
Galit
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AFNI Message Board
Thanks Rick,
I plan to run 3dFWHMx on the residuals I get from 3ddeconvolve, to estimate the ACF parameters for the cluster analysis. I used the BlurToFWHM just for smoothing (before 3ddeconvolve). Is there any reason for keeping or using the ACF parameters from this stage? Or can I safely carry on as originally planned, and estimate it after 3ddeconvolve?
Many thanks again,
Galit
by
Galit
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AFNI Message Board
Hello,
I am running 3dBlurToFWHM, and I sometimes see throught the process an error message:
ERROR: (FAILED) attempt to over-write file 3dFWHMx.1D
I don't see any problem with the output of this function.
What does this error mean? Am I to be concerned?
Many thanks,
Galit
by
Galit
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AFNI Message Board
Hello,
For the -epi_base parameter in align_epi_anat.py, there are the options of mean, median and max. My question is - max(/mean/median) of what? Is it the sub-brick with the maximal contrast? Or is it the maximum of something else?
Thanks,
Galit
by
Galit
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AFNI Message Board
Thanks, Daniel. The two first ways yielded error messages, but downloading and installing the source seemed to do the job! 3dSkullStrip is now finally running!
Thank you also Rick. I will let you know, when I reach the stage of group analysis, if the R packages properly work (the original motivation of this thread).
Best,
galit
by
Galit
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AFNI Message Board
Hi Rick,
This is what I get with ls -l /usr/lib/x86_64-linux-gnu/libgsl.* :
lrwxrwxrwx 1 root root 35 Oct 29 09:34 /usr/lib/x86_64-linux-gnu/libgsl.so.0 -> /usr/lib/x86_64-linux-gnu/libgsl.so
lrwxrwxrwx 1 root root 16 May 6 2017 /usr/lib/x86_64-linux-gnu/libgsl.so.19 -> libgsl.so.19.3.0
-rw-r--r-- 1 root root 2455464 May 6 2017 /usr/lib/x86_64-linux-gnu/libgsl.so.19.3.
by
Galit
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AFNI Message Board
Hi Rick,
Sorry, my misake in typing here the library name.
Anyway, I get the same error message using 3dSkullStrip - that libgsl.so.0 does not exist. I manually tried to open libgsl.so.0 (in both /usr/lib/ and /usr/lib/x86_64-linux/gnu/), and got a message that the link was broken. I removed the file and re-installed it (using the command lines you suggested on October 15 in this thread). And s
by
Galit
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AFNI Message Board
Hi Rick,
I didn't get there yet, at the moment I have problems with running 3dSkullStrip. I get an error that libgsl.so.0 does not exist. But when I run again sudo ln -s /usr/lib/x86_64-linux-gnu/libgsl.so /usr/lib/x86-linux-gnu/libgsl.so.0 (the command that you suggested to solve the R problem) I get the message:
ln: failed to create symbolic link '/usr/lib/x86_64-linux-gnu/libgsl.so
by
Galit
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AFNI Message Board
OK, great. The R package installation seemed to work now. However, when I evaluate the setup, I still get an error that R packages are not installed. That is weird, because the installation seemed to work smoothly. I tried to install each package separately (phia, afex and brms) and got a note for each package that it was successfully installed on the computer (and a few warning messages that see
by
Galit
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AFNI Message Board
Hi Rick,
Here is the whole output:
-------------------------------- general ---------------------------------
architecture: 64bit ELF
system: Linux
release: 3.13.0-37-generic
version: #64-Ubuntu SMP Mon Sep 22 21:28:38 UTC 2014
distribution: LinuxMint 17.1 rebecca
number of CPUs: 8
apparent login shell: tcsh
shell RC file
by
Galit
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AFNI Message Board
Hi Rick,
It says:
ldd (Ubuntu EGLIBC 2.19-0ubuntu6.5) 2.19
It's from 2014... Is that too old?
Thanks,
Galit
by
Galit
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AFNI Message Board
Hello,
I am trying to install afni on Linux. I am new to Linux, so I have very little knowledge on how things work with it.
When I download the R packaes (using rPkgsInstall -pkgs ALL) I get the following error:
oo Warning:
Failed to load R_io.so with this error message:
Error in dyn.load(ll) :
unable to load shared object '/home/galit/abin/R_io.so':
/lib/x86_64-
by
Galit
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AFNI Message Board
Thank you, Gang!
As you said, I definitely want to control for the variability of RT, and clean out its contribution from the overall variability. Because of collinearity, as you said, I should center within each condition, no matter how I do it. I just wonder about two things (and perhaps I just didn't fully understand your previous answers, so my apologies if so):
1. If the point is
by
Galit
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AFNI Message Board
Right, I now noticed that you did write about centering, sorry. Thanks, that seems like a simple solution to solve this! I understand that the default in -qVarCenters is centering across everything, so I should centre myself within each level, right?
I am still confused, though, about something: what is the gain in adding RT as a random effect? You wrote that it accounts for "RT variabili
by
Galit
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AFNI Message Board
Thank you, Gang!
But then there is only one RT (the average) per condition for each subject. So that makes only four data points per subject to adjust for between-subject variability in RT. Isn't that too little?
Also, isn't it problematic that both Cond and RT are used as predictors but they are highly correlated?
Thanks again,
Galit
by
Galit
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AFNI Message Board
Hello,
I was looking at the documentation of 3dLME, trying to understand if this is what I need for my own data:
My data also has RT per condition per subject, similar to Example2. Originally, I was thinking of adding RTs as a predictor to the analysis, but then I reckoned it was a bad idea as it correlates with the Condition predictor. I see that in Example2 in the documentation, RT is added
by
Galit
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AFNI Message Board
Hi Bob,
Thanks for the advice. Unfortunately it didn't work.. All the other popout windows work just fine (clustering, overlay), but they require a regular left click with the mouse, not a right click. I wanted to say that right-clicks don't work on my AFNI but they actually do - right clicking on a brain image does open a navigation window like it used to be. Right clicking on the s
by
Galit
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AFNI Message Board
Just one minor thing - the 'set p-value' by right-clicking on the slider does not open any chooser window anymore where I could type the p-value. I suppose the OS update somehow deleted this feature - what's the way to get it back?
Many thanks again.
by
Galit
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AFNI Message Board
Thank you Rick and Bob!
the version was XQuartz 2.7.11, and copy-pasting the command that Bob mentioned solved the problem!
So many thanks. Happy 2017!
Galit
by
Galit
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AFNI Message Board
Hi,
I have updated my Mac's OS, and ever since AFNI doesn't work properly. Every time I open the GUI and want to add an overlay, for instance, the window from which to choose a file looks very small such that I can't read the list from it but I must enlarge it. When I choose a file there is no "Apply" button etc. When I close the window the whole program shuts down.
A
by
Galit
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AFNI Message Board
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