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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
Page 4 of 5
Pages: 12345
Results 91 - 120 of 137
The file "dfile_rall.1D" is located inside the folder of preprocessed time-series from AFNI proc. This file has 6 columns of datapoints. Each column represents one of the 6 motion parameters:
Three for translation:
- y-axis
- x-axis
- z-axis
Three for rotation:
- pitch
- yaw
- roll
My question is which column (1 to 6) corresponds to which translation and rotation paramete
by
Philipp
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AFNI Message Board
Dear all,
I am processing a clinical dataset. Normally, I run SSwarper first. Then, in a second step, I provide the processed files from SSwarper to AFNI proc (as it is suggested by you AFNI people). However, the alignment was very bad using this approach. tried out all kinds of cost functions too. There was no way to get a proper alignment for the functional/EPI files. The brains were always
by
Philipp
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AFNI Message Board
Here is an update on subject 1, the subject with the massively misaligned skull and brain.
I ran SSwarper again with the following changes in the script:
-deoblique_refitly # This was already added before, but I left it in just in case
-cost_nl_init nmi # I changed this function from "lpa" (standard if not differently specified) to nmi.
Now the brain (and the skull) looks nor
by
Philipp
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AFNI Message Board
Dear all,
I ran SS Warper over a dataset of 21 subjects. The results are perfect, except for two subjects. Lets call them subject 1 and 2.
- Subject 1: in the quality control images of the file the whole head (skull plus brain) looks totally deformed after running SS Warper. Then, I ran skullstripping again but with adding "-deoblique" first, and "-deoblique_refitly" in
by
Philipp
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AFNI Message Board
Hi Gang and Rick,
Gang, thank you. Your solution for AFNI worked fine. I totally forgot that it is possible to select columns with 1dcat. So what your approach with AFNI does is the following:
1. 3dmaskdump: Extraction of all voxels from all subjects into one .1D file. This file contains as many columns as subjects. Each column contains the voxels from one specific subject.
2. Transpose all
by
Philipp
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AFNI Message Board
Dear all,
my aim is to create a single .1D or .txt file containing all voxels’ values in one column, but from many subjects. Using 3dmaskdump, I am only able to do one of the following two options:
- I provide all subjects as input and write the results into one .1D or .txt file. In this case, each subject’s values are added as a new column. The result is a file that contains as many columns
by
Philipp
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AFNI Message Board
Hi Gang,
I will try to explain my question more precisely.
1. I measured/calculated the Power-Law Exponent and the Mean Frequency of fMRI runs.
2. Then, I calculated their correlation via 3dTcorrelate. As you know and already stated, the output of 3dTcorrelate is the correlation for every voxel in the brain, i.e., on a voxel-wise level.
3. I used different ROIs to calculate the average co
by
Philipp
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AFNI Message Board
Hi Rick,
I just checked my .zshrc file. Yes, you are right, the file is accordingly updated by AFNI too. Great. See/read you around.
Philipp
by
Philipp
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AFNI Message Board
Dear all,
I managed to solve the problem. I reinstalled everything again (two times). It somehow works now. However, please let me know if the adjustment of the code that is written for tcsh and bash in my first post can be adapted to zsh. Thank you.
Philipp
by
Philipp
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AFNI Message Board
Dear all,
after already reinstalling AFNI a couple of times on my old laptop (due to some bug fixing problems back then) I thought that I would easily handle the installation of AFNI on my new laptop, since I know it by heart. Well, a new laptop led to new problems.
It is a 2021 MacBook with the current MacOS 12.0.1 Monterey. I use the Zsh shell, but I face the following problem with using
by
Philipp
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AFNI Message Board
Dear all,
I have calculated the correlation between 2 measurements/variables. The result of this correlation is a voxel-wise dataset that shows the correlation for each voxel in the brain. Furthermore, I use different ROIs in the brain.
What I would like to do now is to statistically compare if various correlations between different ROIs significantly differ. This means that I would like t
by
Philipp
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AFNI Message Board
Hi,
I think that you are right. I have to use a scatterplot instead of a correlation matrix. There are many ROIs and for each ROI I would like to calculate the correlation between AF and PLE. This correlation should reflect the mean over all subjects for each ROI (and not values for single subjects).
Each value/point/position in the scatterplot would represent the correlation between AF and
by
Philipp
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AFNI Message Board
Dear all,
I checked the AFNI program list and it seems that 3dNetCorr is the current best (and only?) way to create a correlation matrix in AFNI. I would like to create the following correlation matrix:
- A correlation between the Average/mean Frequency (AF) and the Power-Law Exponent (PLE).
- Different ROIs. The ROIs represent the dots/measurements in the correlation matrix for all subjec
by
Philipp
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AFNI Message Board
Hi,
thanks for the responses (also via email). Rick, you are right. I thought that censored volumes/TRs will also be censored from the errts file (visually in the AFNI GUI!), so that I would see a "string" of the remaining volumes in the errts file after preprocessing in AFNIs GUI.
One more question came up. Out of my 25 subjects 2 subjects showed heavy head motion.
- Subject 6:
by
Philipp
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AFNI Message Board
Hi,
I am having a small problem here with only 1 subject out of a dataset that contains 25 subjects. I ran the following preprocessing script for a resting-state session (one run per subject).
afni_proc.py \
-subj_id ${subject}_Rest \
-out_dir $directory/Results \
-dsets \
$directory_raw/restto3d+orig \
-blocks despike ricor tshift align tlrc volreg mask blur regress \
-copy_anat $di
by
Philipp
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AFNI Message Board
Dear Rick,
this is very good information. In fact, the solution to question number 2 was much easier than I thought. Both options, that is, the one via the GUI and the one via the -batch method work now.
I would have another question beside question 1 in my first post, also in relation to this topic. My dataset contains 25 subjects and I am analyzing three sessions:
- One resting-state
by
Philipp
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AFNI Message Board
Hi Rick,
I uninstalled and reinstalled AFNI a couple of times now. The current status of the problem is as follows.
The command line "export DYLD_LIBRARY_PATH=${DYLD_LIBRARY_PATH}:/opt/X11/lib/flat_namespace" is added in my ".zshrc" file.
The message output by afni_system_check.py -check_all "please set DYLD_LIBRARY_PATH to include /opt/X11/lib/flat_namespace&qu
by
Philipp
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AFNI Message Board
Dear all,
I wrote the following script shown at the end of my post to utilize resting-state FC measurements via AFNI. I have some basic questions concerning FC calculation. Some facts about my dataset and preprocessing with AFNI_proc:
- TR=1s
- No bandpassing in AFNI_proc
- Physiological nuisance regression (of both respiration and cardiac signals) via RetroTS and the subsequent embedding o
by
Philipp
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AFNI Message Board
I will revive this thread since I ran into the same (or into a very similiar problem).
My aim: I wanted to use 3dLME for a second-level analysis. AFNIs 3dLME explanation (https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dLME.html) explains that it is required to upgrade R via the following terminal code: "rPkgsInstall -pkgs ALL".
The problem: Using the command above, the term
by
Philipp
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AFNI Message Board
Here is an update that breaks down the problem into something more comprehensible.
I used the .errts file (the preprocessed output of a resting-state run) as input to calculate both the FFT and the PLE. In my first post in this thread I described the problem that the PLE values always turned out to be way too low (both for single subjects as well as for an average over all subjects).
Then,
by
Philipp
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AFNI Message Board
Dear Gang,
thanks for the response and information.
Philipp
by
Philipp
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AFNI Message Board
Dear all,
I have a question concerning 3dPeriodogram and its use for the calculation of the Fast Fourier Transform (FFT) to subsequently calculate the Power-Law Exponent (PLE).
Question 1: What value (or range of values) is reasonable for the -nfft option? The number of time steps in the runs is 360 and 1180, respectively. Bandpassing is 0.02 to 0.2 Hz for both runs.
Question 2: How should
by
Philipp
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AFNI Message Board
Ok, Rick, an update. AFNI just continued with the preprocessing (it provides me with new output in the terminal), but it is still working on subject1.
I am sorry if this thread might be silly from me, because the reason probably is that my laptop is just extremly slow. I already feel a bit bad for this. But can this really be? I mean that it is THAT slow for the 6 task-based runs compared to t
by
Philipp
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AFNI Message Board
Dear Rick,
I started AFNI_proc again last evening to let it run overnight. Now, around 14 hours later, it is still processing subject1 (as you can see on the screenshot below). This screenshot also shows you where AFNI seems to be stuck.
Additional information:
- AFNI_proc took around 1 hour for the resting-state run per subject. Number of time steps (resting-state): 360.
- Now lets compa
by
Philipp
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AFNI Message Board
Hello Rick,
thanks for the tip with -regress_compute_fitts. I will use it for the genuine task-based session. One question: -regress_compute_fitts should not change anything concerning the time needed by AFNI_proc in my script shown in the first post, correct? Thats because no fitts file is created here anyway, as the GLM is missing and I preprocess the task-based runs "as if" they w
by
Philipp
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AFNI Message Board
Dear all,
I ran upon a strange problem. Let me provide you with an overview first:
- A resting-state analysis (preprocessing) was done for a resting-state run (1 run per subject; 25 subjects overall). This session also included running SSwarper.
- Now I would like to apply the same script for a task-based session (6 runs per subject instead of 1 run as above). Note: why do I apply a "
by
Philipp
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AFNI Message Board
Dear all,
I have a theoretical question concerning the averaging of multiple runs in a task-based design. Imagine that I would like to calculate variables such as functional connectivity, fast fourier transform (and then the power-law exponent), etc. after the preprocessing with AFNI_proc is done.
Options:
1. Should I first use 3dmean to average all runs (for each subject). E.g., there are
by
Philipp
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AFNI Message Board
Dear all,
I read the "Simple Correlation Analysis" introduction from AFNI here: . My question is if it is save to use my already preprocessed resting-state as well as task-based runs to do FC calculations via AFNI on these runs. If I do that, would it be correct to skip step 1) and 2) from the link above, since the raw runs are already preprocessed (bandpassed, nuisance regressed, et
by
Philipp
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AFNI Message Board
Dear Rick,
thanks again for your help. I really appreciate that you help me here so often. And I am giving everything to learn AFNI.
Have a good weekend,
Philipp
by
Philipp
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AFNI Message Board
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Pages: 12345