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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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Hi Paul,
I denoised my functional data using a combination of cosine regressors and CompCor components. My understanding is that it will high-pass filter the data. In this case, it will be innacurate to run 3dRSFC on already high-pass filtered data, right?
However, what if I use the not-denoised data but include the cosine regressors (using 128s cutoff) and CompCor components in the ort f
by
samw
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AFNI Message Board
Hi Rick,
Do you mind if I ask a few more basic questions?
1. How many regressors do you find reasonable to include? I notice that I'm running 3dTProject with a few dozen regressors, and I'm concerned this might affect the quality of the projected data. Will more regressors have a negative impact on the data's quality, or is there absolutely no relationship?
2. Is 3dTProject do
by
samw
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AFNI Message Board
Thank you Rick!
The mean+tlrc you mention is the average of the time series that I pass to 3dTProject, and the errts+tlcr is the output from 3dTProject, is that right?
So if bold_orig_ts.nii.gz are the raw time series, then:
3dTproject -input bold_orig_ts.nii.gz -polort 1 -prefix bold_project.nii.gz
3dTstat -mean -prefix mean_bold_orig.nii.gz bold_orig_ts.nii.gz
3dcalc -a bold_project
by
samw
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AFNI Message Board
Hi Rick,
One reason might be running statistical analysis on software that expect contrast in the images, because when I tried it with the output from 3dTProject it failed. But I understand there is no possibility to switch off demeaning, right?
Best regards,
Sam
by
samw
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AFNI Message Board
Hi Rick,
Is it somehow possible/reasonable to bring back the contrast? I'm using the default polort, should I simply add the mean of each voxel's time series after running 3dTProject?
Best regards,
Sam
by
samw
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AFNI Message Board
Hello!
Is there a default value for the parameter -bandpass in 3dTProject?
I ran the commands
3dTproject -input bold_orig.nii.gz -polort 1 -prefix bold_project_1.nii.gz
3dTproject -input bold_orig.nii.gz -polort 1 -prefix bold_project_2.nii.gz -bandpass 0 1
I expected bold_project_1 and bold_project_2 to have exactly the same voxel values, but they don't, so I'm wonderin
by
samw
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AFNI Message Board
Hi Rick,
Thank you for your reply!
Yes it's a single subject analysis and I'm using the output of 3dTProject to compute RSFC (outside afni_proc at the moment). I don't smooth my data during preprocessing so I assume shouldn't use the blur flag in 3dTProject? Is normalization a good idea though?
Best regards,
Sam
by
samw
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AFNI Message Board
Hi Paul,
No, they don't give the exact same results (although they are not very different), so the question is: shouldn't the results be exactly the same?
The settings to each function are equivalent - detrending, bandpass, removal of orts, etc. The only difference is that in the first case I use 3dTProject to first remove the nuisance time series and then pass the (cleaned) time se
by
samw
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AFNI Message Board
Hi Paul,
Yes, I have already cleaned the time series data with 3dTProject (without band-pass filtering, but with default polort) before 3dRSFC.
Just to be clear then, after I get the cleaned time series with 3dTProject, I can simply run the command
3dRSFC -prefix RSFC 0.01 0.1 -input cleaned_data.nii.gz -nodetrend
and that will appropriately compute the parameters, is that correct?
Bes
by
samw
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AFNI Message Board
Hello!
This is a statistical question rather than afni specific but since I'm using 3dTproject I was wondering what the relationship between polort and high-pass filter is. If I use a polort of 2 it will remove very low frequencies which is what high-pass filtering does, is that correct?
Also why does the 3dTproject help file say "It makes no sense to use a value of pp greater than 2,
by
samw
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AFNI Message Board
Hi Rick,
afni_proc seems to use principal components (PCs) for CSF but what about WM? Why aren't components calculated for WM as well?
Also why are only 3 PCs included? Wouldn't it be better to calculate the number of PCs automatically based on their ability to explain variance in the dataset, as implemented here: (using the variance_threshold option)? Or are there disadvantages in t
by
samw
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AFNI Message Board
Hello!
I'm using 3dTProject and I have some questions after looking at the output from this command:
3dTproject -input bold_orig.nii.gz -polort 1 -prefix bold_project.nii.gz
1. the time-series plots look identical between bold_orig and bold_project but the two images look very different. bold_orig looks like a standard bold image whereas bold_project is more like a homogeneous imag
by
samw
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AFNI Message Board
:D :D :D
Thanks Paul for your (always) helpful response! You should turn it into a paper ;), many important points that I believe many of us are unaware of.
"I think many people have ignored the degree of freedom loss with bandpassing, and it is really a problem in interpreting results"
This comes to the crux of the matter. I suppose this is more a statistical rather than afni ques
by
samw
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AFNI Message Board
Thanks Paul!
I'm using 3TProject to regress out fixed components from resting state data and I use a bandpass filter 0.01 0.1 (TR=2):
I get this output:
++ setting up stopband frequency mask
+ Block #0: 250 time points -- 147 stopband regressors
++ 1 Blocks * 3 polynomials -- 3 polort regressors
+ -- 65 other fixed ort regressors
++ 250 retained time points MINUS 215 regressors
by
samw
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AFNI Message Board
Hi Paul,
Can I ask you another question regarding 3dRSFC please? Will ALFF computation with 3dRSFC be equivalent in these two situations?
1)
3dTproject -input orig_data.nii.gz -prefix cleaned_data.nii.gz -ort nuisance.1D -bandpass 0.01 0.1
3dRSFC -input cleaned_data.nii.gz -prefix RSFC -nodetrend -band 0 99999
2)
3dRSFC -input orig_data.nii.gz -prefix RSFC -band 0.01 0.1 -ort nuisanc
by
samw
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AFNI Message Board
Hello,
I'm trying to calculate degree centrality (DC) and I was wondering if it would be possible to compute DC within an ROI instead of doing it at every voxel. If I use the -mask option, DC is computed for the voxels within this mask. Can I simply average or sum these values to get a global DC for the ROI?
Thanks!
Sam
by
samw
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AFNI Message Board
Hello!
Is it recommended to apply a band pass filter to resting state data with about 2/3mm resolution? I'm not sure if the recommended approach is not to use any filter at all, to use only high-pass filter or use both high- and low-pass filter. I do not have physio recordings.
Thank you very much!
Sam
by
samw
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AFNI Message Board
Hi Paul,
Thank you again for your response! Do you mind if I ask a few related questions please?
I ran the command
3dRSFC -prefix RSFC 0.01 0.1 data.nii.gz
and I got these files:
RSFC_ALFF+orig.BRIK, RSFC_mALFF+orig.BRIK, RSFC_fALFF+orig.BRIK, RSFC_RSFA+orig.BRIK, RSFC_mRSFA+orig.BRIK, RSFC_fRSFA+orig.BRIK (and the corresponding HEAD files).
1 - I'm confused about the -no_rs_out op
by
samw
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AFNI Message Board
Hi Paul,
Thank you very much, that was very helpful.
If I understood correctly, the fALFF output of the 3dRSFC command will contain the bandpassed time series right? You suggested in the previous post that I don't need to use the bandpassed time series later. However if bandpass is required to calculate the LFFs that go into fALFF, then the bandpassed time series should be used if I int
by
samw
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AFNI Message Board
Hi Gang,
When you say that "FMRI data are not suited for causal modeling through GCA" do you mean all kinds of fMRI data (including resting state) or are you specifically referring to task-based fMRI?
I thought the afni tools 1dGC and 3dGC addressed some of the issues of temporal resolution, or am I wrong?
Are you suggesting that we should not perform Granger Causality with any kin
by
samw
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AFNI Message Board
Hi,
I'd like to calculate falff using 3dRSFC. However it seems that 3dRSFC bandpass filters the data which would be a problem for falff. Is there a way to shut off bandpass filtering?
Also is the -ort option equivalent to the -ort option in 3dtproject? I was planning to use 3dtproject to remove nuisance timeseries before computing falff with 3dRSFC but I think I can do it with 3dRSFC dir
by
samw
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AFNI Message Board
Thank you very much Paul for this very informative answer. Everything you said makes a lot of sense. Are there any plans to include 3dLombScargle and 3dAmpToRSFC in the afni_proc processing pipeline any time soon?
Best regards,
Sam
by
samw
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AFNI Message Board
Thanks Rick. Just to be clear, when you say that the time points censored out will be exactly 0, do you mean that the entire volume is converted to zeros? To me the NTRP seems to be the best option since voxel values would be closer to their neighboring volume voxels, is there a particular reason why NTRP isn't the default mode in afni_proc?
Sam
by
samw
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AFNI Message Board
Hi Paul,
Thanks for your response and really nice to know about these two functions. However, just for my understanding, you say I can't combine censoring with 3dRSFC because there are missing time points, but isn't the whole point of the ZERO/NTRP modes in 3dTProject to preserve the same time points as the original time series? If missing time points is the only reason why 3dRSFC ca
by
samw
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AFNI Message Board
Hi,
I'd like to use 3dRSFC and was wondering if I can censor the data with 3dTProject before computing connectivity. Paul mentioned here (https://afni.nimh.nih.gov/afni/community/board/read.php?1,153171,153191#msg-153191) that censoring shouldn't be done when using 3dRSFC, because there will be missing points. But what if I choose the ZERO or NTPR modes in 3dTProject which preserve t
by
samw
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AFNI Message Board
Thank you Cesar, that was very helpful. However why are these two options offered in afni if the two modes are equivalent?
Also I'm assuming that what Bob is referring to when he says "censoring-via-regression" is the ZERO mode in 3dTproject.
In your opinion do you think censoring-via-regression is still the best approach to deal with motion outliers?
Many thanks,
Sam
by
samw
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AFNI Message Board
I understand that afni_proc censors the data using 3dTproject. The default mode seems to be KILL (is it?), which removes time points from dataset. However, I read this post from Bob Cox (https://neurostars.org/t/despiking-vs-scrubbing/2157/10) in which he wrote that adding a regression matrix column with zeros and ones (ZERO mode) and deleting the row (KILL mode) are equivalent. Or am I misunders
by
samw
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AFNI Message Board
Hi,
Can I use @ANATICOR if I have no cardio/physio recordings?
Best regards,
Sam
by
samw
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AFNI Message Board
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