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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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Dear afni experts,
When exploring MRI data with afni, it is often necessary to open multiple linked afni GUI windows in order to see and compare multiple coregisted datasets side-by-side interactively, especially when comparing the impact of different MR sequence, experiment design, or data processing parameters.
Very often, I find myself need to re-open the same set of views (even with the
by
herrlich10
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AFNI Message Board
Sorry, I've overlooked an important detail:
Previously, I tested both subprocess and ! notation in jupyter notebook, and got the single threaded result.
I've just re-tested them in vanilla ipython console, and as rick said, both of them worked as expected with OpenMP enabled.
What's wrong with jupyter notebook, then?
by
herrlich10
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AFNI Message Board
Good news:)
Here is my system info that might be relevant
------------------------------------------------------------
% afni -ver
Precompiled binary macosx_10.7_Intel_64: Nov 23 2016 (Version AFNI_16.3.13)
% system_profiler SPSoftwareDataType
System Version: macOS 10.12 (16A323)
Kernel Version: Darwin 16.0.0
Boot Volume: C
Boot Mode: Normal
Secure Vi
by
herrlich10
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AFNI Message Board
Dear afni experts,
I would like to execute afni commands from python, e.g., using subprocess.check_call() or ipython's ! notation.
However, it seems that commands with OpenMP multithread support, e.g., 3dREMLfit or 3dDeconvolve, only deploy a single thread when executed from python, dramatically slowing down the computation.
For example, when I run
subprocess.check_call(['tcsh&
by
herrlich10
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AFNI Message Board
Thank you Bob for your explanation. I understand you must have a busy priority queue for developing such a complex piece of software.
By the way, do you think upsampling the functional data before 3dvolreg would possibly do any good to motion correction?
Is there an easy way to objectively compare the quality of two sets of motion correction results using afni (e.g., 3dvolreg -dfile would be
by
herrlich10
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AFNI Message Board
Thank you rick for your reply:)
I was fiddling to see whether upsampling a little bit before running 3dvolreg would be helpful for getting more accurate realignment, especially when only a limited portion of the brain is covered in the functional images.
In the above circumstance, I found 3dvolreg actually became the bottleneck in the pipeline, consuming much more time than 3dAllineate and 3d
by
herrlich10
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AFNI Message Board
Dear afni experts,
I have a "Precompiled binary macosx_10.7_Intel_64: Nov 23 2016 (Version AFNI_16.3.13)" version of afni on my Mac Pro, and I notice that some commands (e.g., 3dAllineate, 3dDeconvolve, etc.) are parallelized using OpenMP, making them run considerably faster.
Does 3dvolreg has similar OpenMP support?
If I need to compile afni myself in order to get such functiona
by
herrlich10
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AFNI Message Board
Ok, I see. Thanks for the continuous effort from the afni team for making it better.
I'm new to afni. The link to provide is well written, and that's where I learnt to do the oblique/deoblique stuff:)
by
herrlich10
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AFNI Message Board
Hi, all~
I'd like to rotate a plumb anat to match an oblique EPI (without moving the EPI at all) so that they overlap correctly.
Before operation, 3dinfo said the anat was "plumb" and the EPI was "oblique".
Then I called:
3dWarp -card2oblique EPI -prefix anat -overwrite anat+orig
After the operation, the anat image was rotated as expected, and aligned well with t
by
herrlich10
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AFNI Message Board
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