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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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Hello Rick,
Yes, indeed. Thank you very much for taking a look into the matter. I really appreciate it!
Sincerely,
Ann
by
annschoe
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AFNI Message Board
Here is the result.
achoe2% 3dTstat -absmax -prefix - X.xmat.1D\'
++ 3dTstat: AFNI version=AFNI_21.0.04 (Jan 18 2021) [64-bit]
++ Authored by: KR Hammett & RW Cox
*+ WARNING: Input dataset is not 3D+time; assuming TR=1.0
1
1
0.997748
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0.997736
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0.997717
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1
0.997748
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0.997736
1
0.997717
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0.999994
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0.999994
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0.999994
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0.999994
by
annschoe
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AFNI Message Board
Hello Rick,
Here is the output:
achoe2% 1d_tool.py -show_cormat_warnings -infile X.xmat.1D
-- no warnings for correlation matrix (cut = 0.400) --
Thank you,
Ann
by
annschoe
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AFNI Message Board
Hello, pt.
Thanks for pinging. And as for the bandpass issue - I did read the note, and I agree with you. However, the thought that restings state data should be band passed at 0.01-0.1Hz has been ingrained in people's head so much so that if I say I didn't do it, I am immediately hit back with a lot of skeptical looks and questions - something I don't want to really deal with
by
annschoe
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AFNI Message Board
Good afternoon pt,
Thank you so much for looking into the questions. Below are my responses.
-AFNI version ("afni -ver")?
Precompiled binary macos_10.12_local: Jan 18 2021 (Version AFNI_21.0.04 'Titus')
-One first thing to note about your afni_proc.py command the QC: using "-html_review_style pythonic"
I actually have this line of code in my afni_proc
by
annschoe
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AFNI Message Board
Good afternoon,
I have two questions regarding the quality control report that is generated after running afni_proc.py, which I am using to preprocess my resting state fMRI data set. Please see below for my afni_proc.py
afni_proc.py -subj_id ${subj} \
-script proc.${subj} -scr_overwrite \
-blocks despike tshift align tlrc volreg blur mask regress \
-out_dir $outputDir \
-copy_an
by
annschoe
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AFNI Message Board
Hello pt,
So here are my answers to your questions
- When I type conda env list, the terminal shows that I have python 2.7 activated.
- The reason I showed you the afni_sytem_check results produced in bash, not tcsh (my preferred shell) is that I wanted to let you do a side-by-side comparison of failed and successful results obtained from the same shell. This, because I never had a successf
by
annschoe
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AFNI Message Board
Hello pt,
Not Wheeeeeee :(
I have followed your instruction and conda now runs in tcsh (good). I am now getting error messages in both bash and tcsh (not so good). One thing of note is that in addition to following your instructions, I've also updated afni to the AFNI_21.0.04 'Titus'.
Here is the result of the newly failed afni_system_check, ran using bash
---------
by
annschoe
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AFNI Message Board
Good afternoon,
I have been getting this error message when I run the afni_system_check command:
------------------------------ python libs -------------------------------
++ module loaded: PyQt4
module file : /usr/local/lib/python2.7/site-packages/PyQt4/__init__.pyc
** failed to load module matplotlib.pyplot
-- matplotlib.pyplot is not required, but is desirable
-- python b
by
annschoe
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AFNI Message Board