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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 3 of 5
Pages: 12345
Results 61 - 90 of 137
Hi Paul,
I am not interested in one specific frequency/oscillation; I am not interested in one particular periodicity of the time-series that would then "pop out" to be easily detected in the frequency-domain. Instead, I am interested in the whole frequency spectrum, that is, how the power is distributed, say from 0.01 Hz to the Nyquist frequency.
Now let's get specific (mayb
by
Philipp
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AFNI Message Board
Paul,
thank you for the elaborate answer. What you explained about the properties of a time-series and how these properties can affect the power distribution in the frequency-domain when the time-series is cut at the beginning or end is clear to me.
For example, you wrote that “From that point of view, if you are averaging over frequency windows/bands, *and* your time series has constant st
by
Philipp
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AFNI Message Board
Dear all,
I would like to know if cutting a time-series with 3dTcat (e.g., removing the first 300 TRs in a 3000 TR time-series) yields a minimally different time-series if the cutting is done before vs. after using AFNI proc concerning the power spectrum.
Let me make it more clear with two cases.
1. I cut the time-series before preprocessing with 3dTcat (or I simply use the "-tcat_rem
by
Philipp
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AFNI Message Board
Dear all,
I have a list of single .nii files that need to be combined into one full-length run. Therefore, I am using the command
3dTcat \
-tr 2.16 \
-prefix Run 20160321_204111ep2dboldrestingstates003a001_*.nii
It works fine for all subjects. However, I have one subject with one particular .nii file (number 54 in the list) that causes problems. Here is the output from 3dTcat:
-p
by
Philipp
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AFNI Message Board
Thanks. I completely missed the fact that a couple of folders contain multiple runs, because all other folders didn't.
by
Philipp
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AFNI Message Board
Hi Rick,
nono, what I meant to say was the following: the only thing running was my terminal with AFNI proc. And everything together, the system plus AFNI, used around 15 GB. I have everything closed when running preprocessing.
Thanks for your help so far, your suggestion with the manual polort option works great!
by
Philipp
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AFNI Message Board
Ok, thanks. Anyway, like I wrote before, using a polort degree of 2 in combination with bandpassing somehow works much faster, even though the number of baseline funs in detrending remains more or less the same.
My laptop uses ~15 GB of its 32 GB when running AFNI proc for one subject. I think the amount of Ram needed was the same when using the polort option of 34. However, it seemed to never
by
Philipp
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AFNI Message Board
You mean that I should take out the following parts of the script again?
-regress_reml_exec \
-regress_compute_fitts \
by
Philipp
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AFNI Message Board
Thanks for the explanation.
When adding
-regress_compute_fitts \
to my AFNI proc script, it fails with the following message.
** cannot compute fitts, have 3dD_stop but no reml_exec
** script creation failure for block 'regress'
Any clue what is wrong here? Is something in my script wrong?
...
afni_proc.py \
-subj_id ${subject}_Run \
-out_dir $directory_run/Resul
by
Philipp
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AFNI Message Board
Hi Rick,
yes, some of the runs indeed go up to two hours. These are sleep recordings and subjects were allowed to sleep in the scanner up to two hours.
I will now try running my script again adding
-regress_polort 2 \
-regress_bandpass 0.01 1
as you suggested, thank you. The option -regress_compute_fitts does not work or make sense here, because I use a resting-state script.
U
by
Philipp
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AFNI Message Board
Dear all,
by default, AFNI proc automatically sets the value for -regress_polort
My question is: does the automatic calculation of the polort degree work well (reasonable) when the runs are very long? By very long I mean runs with ~2400 time points (TRs).
For example, I am currently running AFNI proc for such a long run length and it set the polort degree to 34.
Input polort=34; Longes
by
Philipp
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AFNI Message Board
Dear all,
I have a dataset consisting of many .IMA files for each subject. I would like to use AFNI’s Dimon to convert the data over into AFNI’s .HEAD and .BRIK files. This works fine for the anatomical scans, and the results look good too.
However, Dimon fails for all subjects’ functional scans. Here is the output for one subject.
Dimon version 4.29 (February 16, 2022) running, use &
by
Philipp
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AFNI Message Board
Hi,
thanks for the information and thoughts. There is almost no head motion between the single TRs in the raw data. I therefore assume that your thoughts are going in the right direction, namely that the recorded motion could stem from breathing.
by
Philipp
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AFNI Message Board
Hello Osman,
I think what you are looking for is a so called "for loop". The exact code for a "for loop" depends on the shell language that you are using (bash, tcsh, zsh, etc.).
A for loop can be created as follows.
Before the code that specifies AFNI proc, you would have to add the for loop code; something along the following lines:
for subject in Subject1 Subjec
by
Philipp
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AFNI Message Board
Dear all,
I am interested in head motion under anesthesia. As we all know, subjects exhibit variability in head motion when lying awake in the scanner.
Under anesthesia, all subjects of a dataset that I am working on show the same kind of small but ongoing, rapid, and "spike-like" head motion.
Since we can only estimate head motion in fMRI, my question is if the time-series of
by
Philipp
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AFNI Message Board
Hi Paul,
thanks. Changing those values in 3dfim+ does not really change the results. I will drop using 3dfim+ for this purpose now. Instead, and since you said that 3dfim+ is not really designed for my aim anyway, I am going to compute the slope in Python based on the extracted power-spectra computed in AFNI. (Whatever the reason is that 3dfim+ "fails" on this particular preprocessin
by
Philipp
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AFNI Message Board
Hi Paul,
lets start with 3dPeriodogram (and leave 3dLombScargle aside for the moment, just to make things easier). Some facts first:
- I don't bandpass the data (via bandpassing in AFNI proc). I avoid a direct bandpassing to keep DOF high.
- However, once I transformed the preprocessed time-series into its frequency-domain via 3dPeriodogram, I cut the frequency domain via 3dTcat to 0.
by
Philipp
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AFNI Message Board
Dear all,
this is going to be a longer post, but it is necessary to explain the problem and the single steps that probably brought it up.
I am interested in the power-law exponent (PLE). What is the PLE? The PLE, basically, is the slope of a linear regression applied on the log-log transformation of the frequency-domain. Without going into detail here, the general steps to compute the PLE a
by
Philipp
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AFNI Message Board
Dear all,
AFNI proc fails to properly align the EPI to the anatomical dataset for one specific subject. The resulting EPI brain by AFNI proc is completly misaligned.
Here is how I proceeded.
First, deoblique was required because the dataset was very oblique.
3dcopy $directory_raw/anat1to3d+orig Temporary
3drefit -oblique_recenter Temporary+orig
3drefit -deoblique Temporary+orig
3
by
Philipp
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AFNI Message Board
Hi Paul and good morning,
the output of
cat out.ss_review_uvars.json
is
{
"afni_package": "macos_10.12_local",
"afni_ver": "AFNI_22.1.01",
"censor_dset": "censor_Subject1_Rest_combined_2.1D",
"copy_anat": "anat_final+tlrc.HEAD",
"cormat_warn_dset": "out.cormat_warn.txt&
by
Philipp
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AFNI Message Board
Here is yet another update. What I did in order to fix the problem with the "libjpeg.9.dylib" file was the following.
- I found this file under my AFNI installation (/Applications/AFNI/abin).
- I then copy-pasted the file libjpeg.9.dylib to /usr/local/lib
This folder is one of the three folders where AFNI tried to search this file before, as you can see here
Reason: tried: &
by
Philipp
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AFNI Message Board
Here is an update.
I went back to Rick’s suggestion, i.e., adding the following command to the terminal/shell in order to assign a new path.
ln -s /usr/local/bin/python3 /usr/local/bin/python
However, the OS then prints a “permission denied”. I googled a bit more and found out that there is the possibility of adding the command "sudo" just before the command that Rick suggeste
by
Philipp
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AFNI Message Board
Hi Paul,
the output of
# A:
\ls -l /usr/local/bin/python3
# B:
\ls -l /usr/local/bin/python
is
zsh: command not found: #
lrwxr-xr-x 1 root wheel 70 Apr 3 19:44 /usr/local/bin/python3 -> ../../../Library/Frameworks/Python.framework/Versions/3.10/bin/python3
zsh: command not found: #
ls: /usr/local/bin/python: No such file or directory
True, you are right about your c
by
Philipp
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AFNI Message Board
Hi,
this is the output of afni_system_check.py -check_all:
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 21.4.0
version: Darwin Kernel Version 21.4.0: Fri Mar 18 00:46:32 PDT 2022; root:xnu-8020.101.4~15/RELEASE_ARM64_T6000
distribution: 12.3.1
number of
by
Philipp
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AFNI Message Board
Paul,
I googled a bit more and found out that many people have this problem since the latest big Mac OS update when Python 2.7.16 was removed from the OS. This problem is not just related to AFNI or caused by AFNI, as you already pointed out, but the problem appears with all kinds of programs that use Python.
One solution is to simply reinstall Python 2.7.16 (the version that came with Mac
by
Philipp
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AFNI Message Board
Here are the outputs.
ls -s /usr/local/bin/python3.10 /usr/local/bin/python
ls: /usr/local/bin/python: No such file or directory
304 /usr/local/bin/python3.10
ls /usr/local/bin/python*
/usr/local/bin/python3 /usr/local/bin/python3-intel64 /usr/local/bin/python3.10-config
/usr/local/bin/python3-config /usr/local/bin/python3.10 /usr/local/bin/python3.10-intel64
ls -d /Libr
by
Philipp
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AFNI Message Board
Paul,
I realized that Python 2.x is not installed on the system anymore. I was a bit shocked to see this, since it was the system’s default. A quick google search provided me with the information that Apple indeed removed Python 2.7.x with one of their latest OS updates (that I installed).
Probably this is the reason why AFNI now fails everytime it needs Python (even though I ran my termin
by
Philipp
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AFNI Message Board
Hi Paul,
I am happy to see you here and helping me out. I am really sad to be stuck again. :(
Here are the outputs of the codes that you suggested
which python
python: aliased to /usr/local/bin/python3
\ls -l `which python`
ls: aliased: No such file or directory
ls: python:: No such file or directory
ls: to: No such file or directory
lrwxr-xr-x 1 root wheel 70 Apr 3 19:44
by
Philipp
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AFNI Message Board
Dear all,
I am trying to preprocess data and receive the following problem "env: python: No such file or directory" once AFNI should apply "align_epi_anat.py" in my preprocessing script. The same problem appears when using SSwarper. From my understanding, the problem basically appears everytime AFNI has to use Python.
In this topic people reported the exact same problem
by
Philipp
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AFNI Message Board
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Pages: 12345