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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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Hi Daniel,
Thanks for the reply. I would love to be able to build regularly but I often run into glitches that I don't have time to resolve. I need the whole package to run seamlessly, including dependencies on R_io.so.
If you have new tools to automate the build I would be happy to test them out.
In the meanwhile, I grabbed the dicom_ programs from the version that worked and that see
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Ziad Saad
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AFNI Message Board
Hi Daniel,
Any thoughts on this problem?
All the best,
Ziad
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Ziad Saad
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AFNI Message Board
Hi Daniel,
I am running Monterey (12.6.3).
macos_10.15_local_gcc_clang/dicom_hinfo works fine!
All the best,
Ziad
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Ziad Saad
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AFNI Message Board
Hi Daniel,
This is happening on a mac pro 2019, Intel Xeon W. The command is failing in zsh and I am using iTterm2 , but the dicom_hinfo command also fails from Terminal, whether using zsh, sh, or tcsh.
Cheers,
Z
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Ziad Saad
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AFNI Message Board
Hi Rick, Daniel,
Glad I managed to provide some intrigue.
The head command works fine.
Cheers,
Z
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Ziad Saad
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AFNI Message Board
Hi Rick,
Good points but no cigar, the below has a script to reproduce the problem. It assumes you have AFNI_demo/CD under your home directory (where else would it be?).
My afni version is: Precompiled binary macos_10.12_local: Oct 1 2022 (Version AFNI_22.2.12 'Marcus Aurelius')
Thanks!
Ziad
#!/bin/sh
crazypath=${PWD}/tmp/Volumes/ns2/MyFavoriteThings88/healer/transfer/BC
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Ziad Saad
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AFNI Message Board
Dear Friends in AFNI,
I hope all is well.
dicom_hdr and dicom_hinfo are crashing with the below error when provided with long dicom filenames (~255 chars).
I thought the problem was in THD_zzprintf but I was wrong. Not sure what is causing this.
Cheers,
Z
Error message:
zsh: illegal hardware instruction dicom_hdr
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Ziad Saad
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AFNI Message Board
Dear AFNI Colleagues,
I need to smooth multiple data sets to the same level of smoothness that I estimate using 3dFWHMx . I apply the smoothing with 3dBlurToFWHM and provide the input dataset for -blurmaster and -detrend, which is fine for datasets with more than one time frame.
However, in the cases where only one frame is available, 3dFWHMx has -2difMAD to provide an estimate of smoothne
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Ziad Saad
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AFNI Message Board
Hi Daniel,
In line below:
Cheers,
Z
Daniel Glen Wrote:
-------------------------------------------------------
> Since this is smb, try adjusting the buffer size
> in smb.conf.
Any tips for how that is done and whether I should adjust up or down?
> This was still in a single script
> that did things sequentially, and 3dTstat was one
> of the steps?
Correct.
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Ziad Saad
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AFNI Message Board
I spoke too soon.
The error has reared up again. This time on a 3dTstat command in a different dataset and without scripts running in parallel.
For whatever it is worth: The numbers below ++ WARNING are identical to the previously reported error. I suspect they reflect i/o buffer size and initialization.
All the best,
Ziad
++ 3dTstat: AFNI version=AFNI_22.1.14 (Jun 24 2022) [64-bit]
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Ziad Saad
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AFNI Message Board
Thank you, Daniel.
I will try to debug with your suggestions in mind next time I have a chance to reproduce the problem. As I mentioned to Peter, there are a lot of scripts being invoked and they all assume nii.gz output so modifications for compression options will take time to implement and test.
Let's hold off on digging deeper until either I or others who encounter this problem can
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Ziad Saad
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AFNI Message Board
Hi Peter!
Responses inline below.
All the best,
Ziad
Peter Molfese Wrote:
-------------------------------------------------------
> Just curious if there are some network properties
> that we could also use to debug things:
>
> 1) You're using MacOS?
YES
> 2) What protocol is the network share? NFS? SMB?
SMB
> AFS?
> 3) How big are the files?
~ 5-10
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Ziad Saad
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AFNI Message Board
Thank you, Daniel.
I am afraid the sleep option is not practical for me -- not sure where to put it as the problem occurs at multiple spots. I will need to dig deeper to find out how to replicate the problem with regularity.
To be clear, all the read-write operations carried out by each process are sequential. Think a large number of scripts running on each subject separately and outputs are
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Ziad Saad
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AFNI Message Board
Thank you, Daniel.
I will try pigz and see if things get better.
I am intrigued by the delay suggestion and it got me wondering whether it is possible to trap for this error within AFNI's I/O and have the operation sleep for a bit before trying again, but only when needed. I suspect this problem occurs more often when using network file systems and when running parallel processes with
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Ziad Saad
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AFNI Message Board
Dear friends,
Following up on the nifti_read_buffer error. I am getting it sporadically when I run multiple processes in parallel. Rerunning the same command (one process) works fine. I wonder if this is an OS limitation.
A sample output is shown below, the ellipses in the path are mine to make the output more readable:
cheers,
Z
++ 3dcopy: AFNI version=AFNI_22.1.14 (Jun 24 2022) [
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Ziad Saad
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AFNI Message Board
Thank you, Rick!
BTW: I love the new AFNI installation process for macs.
Cheers,
Ziad
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Ziad Saad
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AFNI Message Board
Dear friends in AFNI,
I have been having trouble with R loading R_io.so. Namely, dyn.load('~/abin/R_io.so') returns the message below. Setting 'DYLD_LIBRARY_PATH' in my shell environment (zsh) has no effect. Similarly, setting DYLD_LIBRARY_PATH in my .Rprofile does not change the outcome.
The library in question (here libjpeg.9.dylib) is in under ~/abin/ . How can I ma
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Ziad Saad
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AFNI Message Board
Dear AFNI literati,
I can use your help with a couple of questions:
1- AFNI is taking a long time to startup because it is scanning a large number of CSV files that I don't need to have scanned. I realize I can use -nocsv to turn this off but is there a way to do so with an environment variable?
Update:I have added an ENV to disable csv scanning at startup with: GLOBAL_argopt.read_tcsv
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Ziad Saad
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AFNI Message Board
Hi Rick,
Works great, as prescribed, thank you.
Merry Christmas and Happy New Year!
cheers,
Z
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Ziad Saad
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AFNI Message Board
I do declare, PT: Santa don't do clusters.
However, compiling a local version worked great, libgsl was all that was missing.
Merry Holidays to the whole AFNI team, you guys rock!
Z
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Ziad Saad
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AFNI Message Board
Dear AFNI,
I am looking to run 3dNetCorr (Precompiled binary linux_openmp_64: Dec 20 2021 (Version AFNI_21.3.13 'Trajan')) on a linux cluster, but I do not have libgsl.so.0 no do I have root privileges to install it. Is there a workaround for this?
Ho, Ho, Howly yours,
ZXu
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Ziad Saad
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AFNI Message Board
Dear Colleagues,
Janssen Research and Development, L.L.C., a member of Johnson and Johnson's Family of Companies, is recruiting for a Principal Scientist to analyze biomarker data in support of Janssen Neuroscience clinical trials with the goal of generating signatures that inform on disease stage and biology, mechanisms of drug action, patient subtype and response to treatment.
For a
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Ziad Saad
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AFNI Message Board
You guys are just great, thanks a lot. I will test and report.
Take care, stay safe.
Z
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Ziad Saad
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AFNI Message Board
Ahoy amigos!
I hope you are healthy and sane.
Related to Catalina installations. AFNI binaries installed fine for me, but loading R_io.so fails to load with the following:
Error in dyn.load(ll) :
unable to load shared object '/Users/zsaad/abin/R_io.so':
dlopen(/Users/zsaad/abin/R_io.so, 6): Library not loaded: /sw/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/li
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Ziad Saad
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AFNI Message Board
Dear Afni connoisseurs,
I hope this finds you healthy and operational.
Say I have three datasets: A.nii.gz, B.nii.gz, and C.nii.gz where
B.nii.gz is an anat in orig space
A.nii.gz is an MNI-space version of B.nii.gz created with 3dAllineate and 3drefit -view +tlrc -space MNI . AFNI recognizes it as such, so far so good.
C.nii.gz is a functional dset in orig space
The problem is that w
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Ziad Saad
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AFNI Message Board
Hi Daniel!
Thanks for your help. A->B is as an affine transformation in my original post.
I understand correctly, the process you suggest will involve recomputing the NL transformations, otherwise the whole procedure can be scripted from existing output, correct?
Best,
Ziad
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Ziad Saad
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AFNI Message Board
Hello Veronica,
You can create your own semi-inflated surfaces when you run @SUMA_Make_Spec_FS with the -inflate option. By default the script uses -inflate 200, try adding -inflate 250 and -inflate 300 and see how that works for you.
If you want to do this manually, which would be much faster, look at the code for @SUMA_Make_Spec_FS in the block starting with comment: #and make semi inflat
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Ziad Saad
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AFNI Message Board
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