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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 5 of 5
Pages: 12345
Results 121 - 137 of 137
Dear Rick,
does this mean that I do not have to use scaling for a standard resting-state analysis?
Thanks,
Philipp
by
Philipp
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AFNI Message Board
Dear all,
I am currently stuck on the problem that my resting-state analysis with afni_proc.py results in a flawed outcome. This problem only occurs for my resting-state runs (for all subjects) and not for the task-based runs. The results of the latter are fine.
The problem is that when I open my errts file (e.g. "errts.Subject1_Rest.anaticor+tlrc") there is activation all around
by
Philipp
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AFNI Message Board
Dear Rick,
thank you for taking your time again in order to help me here. I just tried your slightly changed code and it worked via Zsh! No errors or problems occured. And I didn't know that square brackets are treated just like wildcards by AFNI. I knew about the * and ? wildcard option. But, as I said, I did not know that the same applies for the square brackets. And this is why I have
by
Philipp
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AFNI Message Board
An update:
I think that my code to merge the distinct time windows (of the self and non-self runs) is a disaster. With the code displayed in my first post, AFNI would try to do the following:
1. It would assume that it has to take each time window in the two for loops (for SelfTimeWindows & for NonSelfTimeWindows) and resave them under the output names of SelfTimeWindows and NonSelfTime
by
Philipp
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AFNI Message Board
Dear all,
I am back again with another question. I am using Zsh for my terminal on a MAC. Since I got used to the language of Zsh in my learning process of AFNI, I would like to stick to it, even though I read around here that you, the AFNI people, recommended to use tcsh. In case you want to comment on this, please, go ahead. I am interested in case you would still suggest to switch to bash,
by
Philipp
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AFNI Message Board
Update:
The problem is solved. Here is a efficient code which functions.
directory=/users/philipp/desktop/fmri/dataset/subjects
for subject in subj1_exp1
do
for fMRIruns (fitts.Subject_1+tlrc)
do
for TimeWindows ('[21..75]' '[199..253]' '[427..481]' '[489..543]' '[549..603]' '[659..713]' '[837..891]' '[893..947
by
Philipp
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AFNI Message Board
An update:
I just realized that I could simply add 3dTcat as program over and over again, like in the following example (which paradigmatically only shows two time windows):
directory=/users/philipp/desktop/fmri/dataset/subjects
for subject in subj1_exp1
do
for fMRIruns (fitts.Subject_1+tlrc)
do
cd $directory/$subject/Preprocessing
echo "Processing $subject ..."
3dTcat \
by
Philipp
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AFNI Message Board
Dear all,
I am currently working with 3dTcat and my aim is to cut out distinct time windows from a run and then, in a second step, to save those time windows not into one single new file, but into distinct files.
In other words: there is one input file (a preprocessed and regressed run "fitts.Subject_1+tlrc"). I would like to cut out several sub-brick distances (time windows) in thi
by
Philipp
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AFNI Message Board
Thanks, Daniel. I will take a look at 3dLombScargle.
Have a good rest of the week.
by
Philipp
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AFNI Message Board
Another update.
With massive amount of help from a friend of mine, I managed to finally calculate the PLE (for each voxel). I will show you my script here for two reasons:
1. Maybe you have comments on the script.
2. Maybe the script, even though it is a very basic and simple script at this point (and there is tons to improve), could help other beginners who search for how to calculate t
by
Philipp
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AFNI Message Board
An update:
I managed to display the output of step 2 (the calculated frequency domain) by adding the command "> Avg_FFT.1D".
Next, I could then easily display the .1D file via the command "1dplot -ok_1D_text avg_fft.1d". AFNI then plots the frequency domain and it is way better to inspect than via the AFNI GUI of course.
However, I am still stuck with the calculation
by
Philipp
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AFNI Message Board
Dear all,
this is a total beginner question, sorry for this one, but I am stuck. Let me explain you what I plan to do:
I have preprossed one run of one subject. My aim is to extract or calculate the power law exponent of this run. How do I plan to do this? Via the following steps:
1. Take the run’s preprossed file (in my case "pb05.Subject_1.r01.scale+tlrc").
2. Calculate the
by
Philipp
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AFNI Message Board
Rick and Paul,
thank you both for the tips. Rick, I removed the bandpass-filtering code and added "-regress_compute_fitts" as you suggested. It worked out. AFNI is no longer stuck on the previously shown point, and it ends the preprocessing successfully. I got all the results and the colorful brains. Finally.
Thanks again, I am really happy now!
Philipp
by
Philipp
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AFNI Message Board
I return to my topic with a new problem. This problem appeard subsequently in the preprocessing pipeline, more precisely in the regression part.
Let me provide you with short background information about what I intend to do:
- One subject
- Two runs
- Two kinds of stimuli (Self vs. No_Self). Both stimuli are presented as trials in each of the 2 runs (unpredictable for the subject which t
by
Philipp
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AFNI Message Board
Dear Paul and Rick,
a big thanks to both of you for your help and information, which I can use in the future. Rick, I also watched many videos of your talks about AFNI on youtube. These were also very helpful to get into AFNI. I wonder why they do not have more views, they were nicely done.
Philipp
by
Philipp
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AFNI Message Board
Dear Paul,
thanks for your input. In case you will find something out about the data files that I send you, please let me know.
Meanwhile, I changed the following line in my AFNI_proc code:
-align_opts_aea -cost lpc+ZZ -giant_move \
to
-align_opts_aea -cost lpa -giant_move \
This solved the problem. Now, the brain in the file "pb03.Subject_1.r01.volreg+tlrc" is normally
by
Philipp
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AFNI Message Board
Dear all,
I set up my own AFNI_proc.py to preprocess fMRI data of one subject. The problem is that the outcome of the preprocessed data, which was preprocessed by AFNI_proc, produces a faulty/strangely misaligned brain as you can see on the screenshot below. This problem does not exclusively appear for one single subject only, but for all subjects of the dataset that I tried to process.
Thi
by
Philipp
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AFNI Message Board
Page 5 of 5
Pages: 12345