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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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Okay, thanks Paul and Rick! I appreciate the response.
Sincerely,
Ian
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brainboi
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AFNI Message Board
Hi AFNI squad,
I was wondering if there was a way to run a new regression in the same results directory without having to re-do the preprocessing, while including the regression and post-regression steps (REMLfit, blur estimation, APQC, etc). I know the -write_3dd_script afni_proc command can create a new 3dDeconvolve script, but not the rest of the steps I listed. Thanks for your help in adva
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brainboi
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AFNI Message Board
Hi Paul,
First, thanks so much for the link to that incredible paper! I just finished reading it all through and it is so helpful.
Second, for our study we are looking at an often high-motion group (ADHD) and a (typically) lower-motion control group. We've deliberated extensively regarding the censor thresholds we should use, given the ADHD group has disproportionately higher levels of
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brainboi
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AFNI Message Board
Hi Paul,
Thanks for the reply, and sorry for the delay! I included the relevant portion of the proc script in my initial message if you'd like to have a look. I ended up removing the 3dLocalUnifize command and that has fixed the issue for the majority of our subjects! I'm not sure why that was causing the problem, but I'm glad the QC looks good now. And we're using LPC+ZZ f
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brainboi
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AFNI Message Board
Hi Rick,
Thanks for the response! I tried 3dSkullStrip instead but the results look the same. In this case though, I do get this in the terminal output:
#++ removing skull or area outside brain
#Script is running (command trimmed):
3dSkullStrip -orig_vol -input ./__tt_vr_base_min_outlier_unif_ts_rs+orig -prefix ./vr_base_min_outlier_unif_ts_rs_ns
oo Warning 3dSkullStrip (SUMA_3dSku
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brainboi
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AFNI Message Board
Hi AFNI team,
I'm having Anat_EPI alignment issues with most of our subjects. For troubleshooting purposes, I've focused on subjects that have the best initial alignment between anat and EPI. For these subjects, when running align_epi_anat.py independently, the output alignment looks excellent regardless of using lpc+ZZ or lpa+ZZ. But, the overlap between anat_final and final_epi_bas
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brainboi
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AFNI Message Board
Hi Paul,
So, our server admin didn't want to change any of the Python/Matplotlib versions tied to the server Linux distributions. However, they recommended a very simple fix to create a virtual environment using Python's venv module to install a newer matplotlib version, which worked perfectly! Thanks for your help and info about that specific Matplotlib version being bugged.
Sinc
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brainboi
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AFNI Message Board
Hi AFNI team,
I'm trying to switch from using the basic html_review_style to pythonic. I am getting some errors during that portion of the processing though and I'm not sure why. Here is the terminal output:
++ FOR: motion_AS1108_enorm.1D: 1 arrays with 512 pts
++ FOR: outcount_rall.1D: 1 arrays with 512 pts
++ Lists of names and yvars match length
*+ No input x-axis; making
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brainboi
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AFNI Message Board
Hello again Paul,
I was hoping to check-in one more time about this. I originally found the solution to this problem from the @auto_tlrc help page. Specifically, here:
"1- Oh my God! The brain is horribly distorted (by Jason Stein):
The probable cause is a failure of 3dWarpDrive to converge.
In that case, rerun the script with the option
-xform shift_rotate_scale.
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brainboi
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AFNI Message Board
Hi pt,
Thanks for the response! I have attached the output here. It looks like the initial alignment is not great. I tested using "-init_xform AUTO_CENTER" with the @auto_tlrc command just to check, but the same result occurred (convergence not being reached and output being warped). And yes, this is an fMRI processing pipeline. I think the "-xform shift_rotate_scale" optio
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brainboi
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AFNI Message Board
Hi again AFNI team,
A common issue with our dataset is having 3dWarpDrive not converge in the @auto_tlrc command which causes very warped volreg. For these subjects, we have to manually re-run them in a new script adding "-xform shift_rotate_scale" to the @auto_tlrc command. However, on the @auto_tlrc help page, it says this is supposed to be done automatically. We are using an up-to
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brainboi
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AFNI Message Board
Thanks so much, Rick! I wanted to double-check the timing files because afni_proc.py gives me the error:
"**file has rows longer than 1
==BAD: file does not look like global stim times"
and I have to use "-test_stim_files no" to get around it, even though the timings are all in a single row. And I will definitely discuss the slice timing issue with our team.
Best,
I
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brainboi
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AFNI Message Board
Hi there AFNI team,
I have a couple of quick questions I was hoping to get clarification on.
1. If a timing .txt file has all of the times listed (globally) from all 4 runs as a row instead of a column, will this still get appropriately interpreted by 3dDeconvolve? We use the "global_times" option as well.
2. When using To3D to convert Dicom files to AFNI, we have thus far spe
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brainboi
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AFNI Message Board
Hello! I am working on my first gPPI analysis and have a question regarding this portion of the AFNI gPPI script as shown on this page:
For obtaining the interaction regressors, this is what is first suggested:
'First create a 1D (one column) file, conditionA.1D, with 0's (at those TR's where condition A does not occur), 1's (at those TR's where condition A occurs)
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brainboi
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AFNI Message Board
Hello! I have a question similar to the one posted here that was never followed up on:
I am struggling to understand what to choose for a sub_TR value for a beginner gPPI analysis I am working on. The experiment I am working on does not have stimulus onset times synced with TR grids, so I believe this is an option I need to use. The example on the help page (https://afni.nimh.nih.gov/CD-CorrA
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brainboi
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AFNI Message Board
Oh, right. Sorry. Here it is.
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 19.2.0
version: Darwin Kernel Version 19.2.0: Sat Nov 9 03:47:04 PST 2019; root:xnu-6153.61.1~20/RELEASE_X86_64
distribution: 10.15.2 x86_64
number of CPUs: 4
apparent login sh
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brainboi
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AFNI Message Board
My summary is just:
* login shell 'bash', trusting user to translate code examples from 'tcsh'
* shell bash: consider sourcing (non-login) .bashrc from (login) .bash_profile
* check for partial install of PyQt4
I tried to make the output into a txt file like it says on the AFNI site but got this error:
Traceback (most recent call last):
File "<string>&
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brainboi
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AFNI Message Board
I get these error messages:
Error: pyqt@4 from cartr/qt4 is given, but old name pyqt was installed from homebrew/core.
Please try to use pyqt to refer to the formula.
To force migration use `brew migrate --force pyqt`.
Error: pyqt 5.13.2 is already installed
To upgrade to 5.14.0, run `brew upgrade pyqt`.
Trying to upgrade gives me the same error as my original message.
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brainboi
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AFNI Message Board
Hey, I am relatively new and have been getting various error messages when trying to install certain things. Usually similar to this (which is what I just got trying to install Pyqt):
Error: Permission denied @ apply2files - /usr/local/opt/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages
I figured it's about time to see if I can get some help. Does anyone know what
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brainboi
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AFNI Message Board
Everything that came up I put in my post. The installation had those error messages and essentially froze and I had to cancel the install. I am wondering if it's related to another issue I had where when I first started using Pycharm it was using old Python 2 instead of Python 3 and I had to and delete things and set it to use Python 3. Might be unrelated but I am unsure.
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brainboi
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AFNI Message Board
Everything that came up I put in my post. The installation had those error messages and essentially froze and I had to cancel the install. I am wondering if it's related to another issue I had where when I first started using Pycharm it was using old Python 2 instead of Python 3 and I had to go and delete things and set it to use Python 3. Might be unrelated but I am unsure.
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brainboi
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AFNI Message Board
Oh okay, thanks. I used to have Python 2 installed because I used that for a class a few years back but I recently upgraded to 3. I thought I had deleted all the Python 2 files but it's possible I may have missed some. Is it possible it is trying to read the old python 2 files (that should be deleted) instead of the new python 3 ones? I apologize again if I am using terminology incorrectly.
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brainboi
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AFNI Message Board
Hey all, I am brand new to AFNI (and largely to coding as a whole). I have been teaching myself Python 3 for the last few weeks and that is mostly the extent of my experience but I am very eager to learn. I am trying to install the app version on Mac OS and received this system error :
" Running afni_system_check.py -check_all
ERROR:root:code for hash md5 was not found.
Traceback (mo
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brainboi
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AFNI Message Board