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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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Pages: 12
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Hello afni experts,
I have a quick question regarding this topic.
I really liked the idea to also evaluate BOLD % signal change in my data as another quality check for motion.
I scaled the data using the code above and before calculating the stdev I would like to detrend it as recommended. For detrending I used the default setting in 3dTproject (so 3 polynomials). When looking at the detr
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carolin31
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AFNI Message Board
Oh I see! Yes that does make a lot of sense now!
Thank you for your help Rick! :))
Cheers
Carolin
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carolin31
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AFNI Message Board
Hello Rick,
sorry to bother you again with this. As I am working through the code I realize that
step 2 should involve calculating the fraction of spikes (spikes above 2.5 threshold) within the ROI for each time point and not the average.
And step 3 and 4 then to apply a threshold for the fraction and count how many time points exceed this threshold.
What afni function can I use to ca
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carolin31
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AFNI Message Board
Hello Rick!
Yes! This is what I envisioned! Thank you very much for your help :)
Cheers
Carolin
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carolin31
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AFNI Message Board
Dear afni experts,
I wanted to follow-up on my question.
Thank you very much in advance!
Carolin
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carolin31
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AFNI Message Board
Hello Paul,
Thank you very much for your reply.
I apologize if I repeat my question but I want to make sure that I made clear that I am trying to summarize the amount of spikes in the HIP based on the spikiness measure āsā (output from 3dDespike). I am wondering if using 3dToutcount is appropriate to do so in this case.
So I am not looking at the raw signal of the time series and try to d
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carolin31
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AFNI Message Board
Hello afni experts,
I would like to follow up on my question here in case my post was overlooked.
I still believe that using 3dToutcount is not the right thing to do in this case because outliers are determined based on calculating the trend of 's' across all time points and calculating the trend of 's' does not make sense to me.
To consider the temporal association,
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carolin31
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AFNI Message Board
Hello Paul,
Sorry for the late reply. I was on a longer break.
Regarding your questions:
A) Yes. I would like to evaluate the spikiness in the HIP before any data processing
B) I guess I am not sure. My thoughts are that I would like to have a QC measure that reflects how 'bad' the HIP as an ROI is affected by motion artifacts. From what I understand motion can affect differe
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carolin31
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AFNI Message Board
Hello AFNI experts,
I was writing before to ask what metric I could use to summarize the spikiness measure in an ROI after using 3dDespike.
What I did so far is using 3dDespike which gave me an output dataset that includes the spikiness measure 's' for each timepoints of every voxel.
I then used 3dToutcount to calculate the fraction of outliers at each time point in my ROI.
Ho
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carolin31
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AFNI Message Board
Thank you!
I was able to successfully create a 1D file for each subject that shows the outlier fraction for each time point for the left and then the right HIP.
How can I now calculate the number of timepoints/volumes that exceed a certain threshold for outliers in the 1D file?
For my analysis I need to have a temporal continuity of the data. This means I can not censor individual volumes.
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carolin31
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AFNI Message Board
Hello afni experts,
I am focusing in my analysis on the HIP and I would like to assess the "spikiness" in the left and right Hippocampus as a quality check in order to exclude subjects that have too many spikes in the HIP. I used 3dDespike with the -ssave option to get the spikiness measure s for each voxel. This is a 3D+time data set. What measure would you recommend for me to extra
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carolin31
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AFNI Message Board
Hello afni experts,
I would like to calculate the tSNR. The analysis I am working on is trying to extract CerebroVascular reactivity from resting state fMRI so the preprocessing of the data is a little different.
I motion correct and blur the data. Then I linear detrend and bandpass filter. And finally I run the regression which includes 6 motion regressors and .
My question is if I want
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carolin31
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AFNI Message Board
Thank you very much for your help guys!
I think the -b did not belong there. Once I removed it it worked !
Thank you very much :))
Cheers
Carolin
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carolin31
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AFNI Message Board
Hello afni experts,
I have a simple question here.
I have for each subject a 3D dataset which is one sub brick that contains only the beta coefficients for each voxel. I need to normalize those coefficients by a reference value which is the averaged signal across all functional volumes and voxels of each subject. (I am following a suggested pipeline to calculate a cerebro vascular reactivity
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carolin31
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AFNI Message Board
Hello afni experts,
I am trying to do an analysis where after a few preprocessing steps I need to run a linear regression where the independent variable is one BOLD signal time course (linear detrended, bandpass filtered and averaged across the whole brain, so only one regressor that I generate beforehand) and the dependent variable is the individual voxel's time course.
This linear reg
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carolin31
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AFNI Message Board
Hello afni experts,
I am not sure if somebody here can help me with the type of problem I have.
Our lab switched recently to a new grid-system where we have to now use singularity and an afni container.
In this new set up I have the issue that although my shell script for generating the proc.py script includes directory paths starting with /mnt/... (referencing to our mounted storage dis
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carolin31
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AFNI Message Board
Hello afni experts,
I have posted this question before
I am using afni_proc.py with the 3dREMLfit option for nuissance regression in resting state. I would like to get as additional output how much variance was removed by the noise model (including the motion regressors, tissue based regressors, drift etc).
The purpose is to evaluate how much variance was removed for each subjects dependin
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carolin31
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AFNI Message Board
Hello afni experts,
I am trying to run proc.py using 3dremlfit with the option -Rerrts. It is a nuisance regression for resting state data.
At the end of the analysis I get the following fatal error: Can't open dataset errts.P1002_REML+org
Looks like the dataset errts.P1002_REML+org is not created because I use the option -Rerrts ?
Can I ignore this error as long as the -Rerrts out
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carolin31
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AFNI Message Board
Hello Gang,
thank you very much for your reply. I tried your suggestion but it still does not output the R^2 stats. Maybe -rout does not output the R^2 stats for the error in resting state? Below is the script that I used:
afni_proc.py -subj_id ${subj}\
-script proc.py_scripts_remltest/proc_${subj}.sh\
-out_dir ${top_dir}${subj}/${subj}.3dDeconvolve_remltest\
-dsets ${func_dir}pb04.P100
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carolin31
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AFNI Message Board
Hello afni experts,
what option can I use in afni_proc.py (in resting state and using reml) to get as additional output how much variance was removed by the noise model (including the motion regressors, tissue based regressors, drift etc). I would like to evaluate how much variance was removed for each subjects depending on the no of nuisance regressors I use.
Thank you very much for your h
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carolin31
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AFNI Message Board
Sorry, I actually have a follow up question!
When I run my script I get a fatal error: Can't open dataset errts.P1002_REML+org
here is my script :
afni_proc.py -subj_id ${subj}\
-script proc.py_scripts3/proc_${subj}.sh\
-out_dir ${top_dir}${subj}/${subj}.3dDeconvolve_reml\
-dsets ${func_dir}pb04.P1002.scale_masked_Despiked_wds.nii.gz\
-blocks regress -regress_reml_exec -regre
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carolin31
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AFNI Message Board
Thank you very much for this explanation! That makes sense to me!
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carolin31
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AFNI Message Board
Hello afni experts,
I have a question regarding the use of -Rerrts output from 3dremlfit for resting state data. I should first mention that I am analyzing resting state data but instead of looking at functional connectivity I want to investigate if BOLD signal variability (calculated with the MSSD measure) increases after an intervention. So the actual amount of variability in the remaining r
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carolin31
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AFNI Message Board
Thank you very much for your help!
I went with the -regress_motion_file option and it worked right away!
Best
Carolin
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carolin31
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AFNI Message Board
Hi Rick,
thanks a lot! It seems to work! The length of my columns is 150 volumes. I can see that those additional regressors are now considered in the regression. There are 10 additional regressors included in X.xmat.1D and in the output script it says:
initial DF : 150 : 100.0%
DF used for regs of interest : 0 : 0.0%
DF used for censoring : 0 : 0.0%
DF
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carolin31
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AFNI Message Board
Hello afni experts,
I have to run my afni pipeline in two steps as I want to take the data after preprocessing and run wavelet despiking on it, and bring it then back to afni to run the regress block (for nuisance regression for resting state analysis). My problem is that for some reasons 3dDeconvolve does not calculate the demean and derivative from the motion regressors. What am I missing in
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carolin31
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AFNI Message Board
Hello afni experts,
I just have a quick question here:
Does afni currently have a template that is based on an elderly population?
Thank you very much in advance!
Best
Carolin
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carolin31
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AFNI Message Board
Hello Rick,
thank you very much for your reply!
So you are saying that with using -regress_extra_stim_files I can only pass in text files that include only one column? So I need to create 10 of those if I have 10 regressors?
Can it be a .txt file or does it have to be .1D?
Best
Carolin
by
carolin31
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AFNI Message Board
Hello AFNI experts,
I am trying to linearly detrend a preprocessed dataset.
I know that it is not recommended to detrend because 3dDeconvolve does a better job but I want to run a CompCor analysis to extract nuisance regressors for wm and csf and they recommend to motion correct and linearly detrend beforehand.
I ran the following: 3dTproject -input pb02.P1002.r01.volreg+orig. -prefix
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carolin31
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AFNI Message Board
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