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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 AFNI,
I have a few questions around the correct implementation of whole-brain cluster correction in AFNI. Given the recent bug identified in 3dclustsim and the subsequent development of some fixes and new tools to improve the accuracy of cluster-wise correction, I’m in the process of revisiting several analysis and want to make sure I am on the right path. FYI - I am using an updated versio
by
Liesel-Ann Meusel
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AFNI Message Board
Hi AFNI,
I have a few questions around the correct implementation of whole-brain cluster correction in AFNI. Given the recent bug identified in 3dclustsim and the subsequent development of some fixes and new tools to improve the accuracy of cluster-wise correction, I’m in the process of revisiting several analysis and want to make sure I am on the right path. FYI - I am using an updated versio
by
Liesel-Ann Meusel
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AFNI Message Board
Hi Gang,
Thanks for your response. I've copied the output below. Of note, I've successfully run both 3dMVM and 3dLME in the past (I *think* using the versions of AFNI and R I currently have installed, but I could be wrong about this). Now, I'm having difficulty getting either program to run.
bash-3.2$ afni_system_check.py -check_all
-------------------------------- general
by
Liesel-Ann Meusel
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AFNI Message Board
Hi,
I'm also getting the same error when I try to run 3dMVM, and after playing around with my model to narrow down the potential issues, I was beginning to wonder if the error message has something to do with the newer R version I'm using (3.2.2).
Was there ever a resolution on this topic?
Thanks,
Liesel
by
Liesel-Ann Meusel
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AFNI Message Board
In the meantime, I've been using 3dLME (with my old AFNI binaries folder) for the analysis I would eventually like to run in 3dMVM. It is quite a large dataset - 1 between subject variable (3 groups, n = 16, 16, 28), and 3 within-subject task variables (each with two levels). I've been getting the following error message when I try to run an omnibus analysis with 3dLME:
R(19088,0xac6
by
Liesel-Ann Meusel
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AFNI Message Board
Hi Rick,
I tried that but I get the same error message.
by
Liesel-Ann Meusel
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AFNI Message Board
Thanks. Just to note, when I try to run 3dLME with the updated AFNI binaries, I get the same message (missing R_is.so). Everything works fine when I use my old binaries folder.
by
Liesel-Ann Meusel
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AFNI Message Board
Hi AFNI people,
I'm getting the following error while trying to run 3dMVM. I'm on a Mac OS 10.8.2, R version 2.15.2, and I just updated AFNI yesterday (downloaded the precompiled binaries ).
***Error:
Missing R_io.so
Error in if (an$type == "BRIK" && !is.na(an$view)) { :
missing value where TRUE/FALSE needed
Calls: process.MVM.opts -> exists.AFNI.na
by
Liesel-Ann Meusel
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AFNI Message Board
Thanks for the quick response. I've played around with the 3drefit command, and it definitely seems to be what I'm looking for; however, no matter what I try, I can't seem to make the orientation of the datasets line up.
The original anatomical dataset that I reconstruct from DICOM to AFNI is in RSA orientation.
When I transform the anatomical dataset from AFNI to ANALYZE, I u
by
Liesel-Ann Meusel
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AFNI Message Board
Hello again AFNI people,
I have been tasked with figuring out a way to import ROI tracings from ANALYZE into AFNI so that we can overlay them onto 3D+time datasets and extract functional information.
After scanning, all of our data was reconstructed from DICOM to AFNI format. Then, for tracing, the anatomical dataset was put into ANALYZE format using 3dAFNItoANALYZE -orient LPI. In ANALYZE
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Liesel-Ann Meusel
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AFNI Message Board
No worries, thanks for looking into it, I really appreciate it!
With respect to the website, I've managed to find what I needed, so not an issue anymore.
Take care,
Liesel
by
Liesel-Ann Meusel
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AFNI Message Board
Hi Ziad,
Thanks for your help. I've come across the following references that may be helpful? The first describes an automatic algorithm for segmentation of the brain and total intracranial CSF (called Exbrain v.2), whereas the second and third compare various methods of estimating ICV. The third article article also describes a method for estimating ICV with reverse MNI brain masking.
by
Liesel-Ann Meusel
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AFNI Message Board
Hi Ziad,
Thanks for your help. I've come across the following references that may be helpful? The first describes an automatic algorithm for segmentation of the brain and total intracranial CSF (called Exbrain v.2), whereas the second and third compare various methods of estimating ICV. The third article article also describes a method for estimating ICV with reverse MNI brain masking.
by
Liesel-Ann Meusel
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AFNI Message Board
Great, I'll definitely play around with 3dseg. Will Ziad weigh in on this thread or should I send him something directly?
Thanks again!
Liesel
by
Liesel-Ann Meusel
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AFNI Message Board
Hi Rick,
Thanks for your reply. Yes, I'm basically looking for everything within the skull (i.e., brain volume+CSF). We are studying an older population and we want to control for premorbid brain size (i.e., before atrophy), and intra-cranial capacity seems to be the ideal way to do this.
I've done some research, and it seems like many of the programs out there (i.e., Freesurfer
by
Liesel-Ann Meusel
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AFNI Message Board
Hello AFNI people!
Two questions: First, is there a method in AFNI for calculating intracranial volume/capacity? (NOT brain volume)
Also, I'm having issues accessing materials on the AFNI website (for example, any of the educational materials). It has been like this for weeks now. I'm getting the following message:
Forbidden
You don't have permission to access /pub/dis
by
Liesel-Ann Meusel
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AFNI Message Board