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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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Pages: 12
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Hi-
Can I get the citation for the particular Monte Carlo simulation algorithm used for the 3dClustsim function and the -Clustsim option?
A reviewer is asking for it.
Thanks in advance,
Jim Waltz
by
James Waltz
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AFNI Message Board
Thanks - so it is trying to writing to a LOCAL HARD DRIVE that is out of space, or a NETWORK DRIVE that is out of space.
I think it could be either.
I will try to clear space on the NAS and run the script from another node, and see what happens.
-Jim Waltz
by
James Waltz
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AFNI Message Board
Hi-
The -clustsim option is not generating all the files it needs. Instead, I am getting errors like these:
sh: line 3: 335536 Killed 3dttest++ -DAFNI_AUTOMATIC_FDR=NO -DAFNI_DONT_LOGFILE=YES -RANDOMSIGN 139 -nomeans -toz -seed 2108850903 2423010168 -nopermute -mask killmask85_resamp+tlrc -setA TT.nKdI2k3VcPM.resid.nii -prefix ./TT.nKdI2k3VcPM.0071.sdat &>/dev/null
by
James Waltz
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AFNI Message Board
Hi Guys-
I'm a little embarrassed to say that the problem was solved by installing R-4.0.0 and pointing R in the direction of the full set of libraries, with:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/data/brutus_data0/lib
I also had to copy over a newer version of “libstdc++.so.6”.
Now R and 3dMVM work.
Thanks for all your help.
-jw
by
James Waltz
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AFNI Message Board
Right. So I figured out that it was '/tmp' that I needed read/write access to, and now I have read/write access to it.
Now I just get a series of errors where AFNI/R are looking for different files/libraries (e.g., the below).
Just seems to be a problem with our (new/old) installation of R.
So far, we have been hunting down those files/libraries, one by one. I don't know h
by
James Waltz
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AFNI Message Board
I appear to be the owner of both the folder that I sit in, and the owner that R sits in. I gave myself read/write privileges to both, but still I get the same error.
Here, the output of afni_system_check.py -check_all:
-------------------------------- general ---------------------------------
architecture: 64bit
system: Linux
release: 3.10.0-862.el7.x86_
by
James Waltz
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AFNI Message Board
Binaries updated, but not specifically for CentOS. I still get the same error about not being able to create 'R_TempDir'.
Here is the output of afni_system_check.py -check_all:
-------------------------------- general ---------------------------------
architecture: 64bit
system: Linux
release: 3.10.0-862.el7.x86_64
version: #1 S
by
James Waltz
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AFNI Message Board
Ok, thanks a lot. Will talk to the peeps who manage our cluster. -jw
by
James Waltz
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AFNI Message Board
Of note, though. I get no errors, if I run the same AFNI package from another node (running Ubuntu, instead of RedHat).
The advantage of using the RedHat node is that I can take advantage of more processors.
by
James Waltz
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AFNI Message Board
Precompiled binary linux_xorg7_64: May 10 2017 (Version AFNI_17.1.04)
by
James Waltz
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AFNI Message Board
No shortage of problems, trying to run AFNI on this machine:
sh TUIT_3dMVM_MU_DXxEXP_SZvNC.sh
('TUIT_3dMVM_MU_DXxEXP_SZvNC.sh' is below)
afni_system_check.py -check_all
File "/data/brutus_data0/freeware/afni/afni_system_check.py", line 279
print g_help_string
^
SyntaxError: Missing parentheses in call to 'print'. Did you mean
by
James Waltz
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AFNI Message Board
Thanks. That helped. But now that AFNI can find R, I get a different error:
Fatal error: cannot create 'R_TempDir'
Do you know where R/AFNI is trying to create 'R_TempDir', so I can request write permissions?
Thanks,
jw
by
James Waltz
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AFNI Message Board
I am running a 3dMVM script on a local machine, and it is taking a very long time. I want to run the next analysis on another node, but that node doesn't have R. So I have to tell AFNI where to find R. Is that set by an environmental variable?
Thanks,
Jim Waltz
by
James Waltz
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AFNI Message Board
I saw Daniel say "I typically use 3dcopy to create NIFTI datasets from AFNI format datasets", in another thread.
I couldn't see how to do that, from the help pages. Are there instructions somewhere else?
Thanks,
Jim Waltz
by
James Waltz
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AFNI Message Board
Thank you. I got it to work, but I was wondering if there is any documentation on the "BrikLoad" function.
BrikLoad asks for Opt, and the demo specfies Opt.Format = 'matrix’.
I wanted to know what the other format options were.
What I basically WANT is a one dimensional array with all elements. I can DO that by selecting the subbriks I want and reshaping the 3D arrays, but
by
James Waltz
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AFNI Message Board
Hi-
This page mentions a Matlab Library that Ziad and Gang once developed:
but the link is bad.
Can someone tell me where that library has gone, or else the best way to currently export voxel-wise beta coefficients as arrays in Matlab or some other general format?
Thanks very much.
Jim Waltz
by
James Waltz
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AFNI Message Board
Hi-
Including the options:
-cost lpc+ZZ -ginormous_move
fixed 4 out of 5 alignments.
My version of AFNI is too old to include -align_opts_aea as an option.
There is still an offending data set, and I was wondering if I could share it with you, along with my script.
This is a script that my data analyst developed about 5 years ago (she has since moved one). I think it was deve
by
James Waltz
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AFNI Message Board
Hi-
Using align_epi_anat.py, I was unable to achieve good alignment, so I did a manual alignment, to make align_epi_anat.py's job easier.
Instead, my brains, which were aligned in original space, became unaligned in Talairach space.
Here is the align_epi_anat.py command I use:
align_epi_anat.py -anat2epi -anat ${subj}_mpra+orig \
-save_skullstrip -suffix _al_junk
by
James Waltz
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AFNI Message Board
Hi-
We have blocks that are not the same length for every subject.
So I was wondering if it is possible to make block-length in the 3dDeconvolve function variable, as in:
3dDeconvolve -input ${sub}-rl-norm_at+tlrc \
-censor ${sub}-motion_censor.1D \
-jobs 8 \
-polort A \
-mask ${sub}-mask_at+tlrc \
-concat /data/brutus_data1/home/jwaltz/ana/pessig/scripts/RLCat.1D \
-num_stimts 12
by
James Waltz
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AFNI Message Board
Hi- I increased the number of jobs to 16, and it only got as far as Slice 35. Is there a way that I can manually allocate more memory, or use less memory for my MVM? Again, I am including 85 subjects in my analysis, with two between-subjects factors (one with 3 levels, one with 2). Functional images are 101 128 x 128 slices, but the mask has about half that many voxels in it.
by
James Waltz
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AFNI Message Board
Hi-
I set up a 3dMVM to run, with 85 subjects and 2 between-subjects factors.
I ran it on a cluster, with 10 jobs, and it got slower and slower, until it finally got stuck at z-slice 69.
The first few slices took seconds to process, and then, by Slice 25, it was 4 minutes, by Slice 50, it was 8 minutes, and after Slice 69, 5.5 hrs after it started, it froze.
Does anyone know what I am
by
James Waltz
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AFNI Message Board
Hi-
Now, when I try to run AFNI, I get:
MacBook-Pro-86:BinaryPE jameswaltz$ dyld: Library not loaded: /usr/X11/lib/libfontconfig.1.dylib
Referenced from: /Applications/AFNI/afni
Reason: image not found
When I type "which libfontconfig.1.dylib", it tells me:
/Applications/AFNI/libfontconfig.1.dylib
How do I tell AFNI to look for that library in the AFNI directory, in
by
James Waltz
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AFNI Message Board
Hi-
Yes, exactly that.
I know that I can use the target program, to read in text and convert it to binary; I was just trying to eliminate that step, if I could.
jw
by
James Waltz
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AFNI Message Board
Hi-
>> Do you mean that you want a binary file output?
Yes. This what I was asking about.
Thanks,
Jim Waltz
by
James Waltz
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AFNI Message Board
Hi-
Is there a way to have 3dMaskAve spit out a time series as something other than text?
I would be interested to export it as floating point, or 32-bit integer, or nifti.
Thanks,
Jim Waltz
by
James Waltz
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AFNI Message Board
Hi-
I discovered that, I am embarrassed to say, and I apologize.
But now I have ANOTHER problem, after the data load:
---
[1] "Great, test run passed at voxel (35, 63, 50)!"
[1] "Start to compute 101 slices along Z axis. You can monitor the progress"
[1] "and estimate the total run time as shown below."
[1] "01/24/18 12:45:20.856"
Installing pac
by
James Waltz
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AFNI Message Board
Hi-
I get the same error, with quotes around the brackets, and if I run it in tcsh. I also did the equivalent of dos2unix to remove possible ^M's.
Why does it think the dataTable is of length ZERO?
Thanks,
Jim Waltz
by
James Waltz
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AFNI Message Board
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Pages: 12