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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 Rick,
I create the file using a series of system calls through matlab. Basically, I build up the dataset using this function:
function [] = udump_and_glue(master,oneDfile,label,fglue)
[~,~] = system(['3dUndump -datum float -prefix temp.nii -master ' master ' -orient RAI -xyz ' oneDfile]);
[~,~] = system(['3drefit -sublabel 0 ' label ' temp.nii'
by
Andrew Salzwedel
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AFNI Message Board
Hello AFNI,
I encountered some strange behavior involving sub-brick selection and the program 3dExtrema. The data file I am analyzing has 7 sub-bricks. The conventional way to select said sub-bricks via AFNI commands is by using file_name.nii'', where n would range from 0-6 (since that is where AFNI begins counting at 0). However, here are some examples from 3dExtrema that have me sc
by
Andrew Salzwedel
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AFNI Message Board
Sorry for the late response, this was indeed the problem!
Thanks!
by
Andrew Salzwedel
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AFNI Message Board
Hello all,
I'm having an issue with 3dNetCorr that I believe might be AFNI version and/or machine dependent. Basically, everything appears to have run correctly and without error but the whole-brain (i.e. WB_Z_ROI_XXX.nii) maps are "empty" and approximately 2KB in size. It's particularly confusing because the other files, including the .netcc file, look normal.
Thought
by
Andrew Salzwedel
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AFNI Message Board
Another work-around, though not ideal, is to install an older version of XQuartz. I finally did it this morning after being fed-up with the weird AFNI behavior (i.e. crash after closing a sub-window, etc).
Here is what I have:
OS X Yosemite v10.10.5
XQuartz 2.7.7
Note, this might have consequences for other software but I haven't run into anything yet.
Andy
by
Andrew Salzwedel
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AFNI Message Board
Replying to my own comment here, but for those using MacOS and MacPorts, you can switch the default python to 2.7 (assuming you have it installed) using:
sudo port select --set python python27
Best,
Andy
by
Andrew Salzwedel
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AFNI Message Board
Thank you for the quick inquiry Rick, you are the best.
Here are outputs you requested:
awdpt800wg3:~ salzwedelap$ which python
/opt/local/bin/python
awdpt800wg3:~ salzwedelap$ python --version
Python 3.4.5
awdpt800wg3:~ salzwedelap$ afni -ver
Precompiled binary macosx_10.7_Intel_64: Feb 25 2016 (Version AFNI_16.0.10)
Indeed, it looks like I'm using Python 3.X...
Andy
by
Andrew Salzwedel
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AFNI Message Board
Following some updates to my computer that were out of my control I get the following error when trying to run afni_proc.py:
awdpt800wg3:~ salzwedelap$ afni_proc.py
File "/Users/salzwedelap/abin/afni_proc.py", line 754
print '%sSubjProcSream: %s' % (mesg, self.label)
^
SyntaxError: invalid syntax
Normally, running this command wou
by
Andrew Salzwedel
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AFNI Message Board
I've become good friends with the 3dMVM program and help file, but recently I discovered something that could potentially undermine said friendship...
What is the difference between using -wsE2 and -wsMVT? I have a within-subject variable with 6 levels and it would seem both are appropriate and/or do the same thing but potentially produce different outputs (testing empirically now...)?
by
Andrew Salzwedel
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AFNI Message Board