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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
Results 1 - 30 of 51
Peter,
Thank you so much for your recommendations.
The scanner is a Phillips Achieva.
Regarding to the @filename, I would like to ask the following. Should the @filename has to be a .1D file containing the time offsets for each slice?
For instance, if I have:
slice order = (1,3,5...35 ; 2,4,6...34)
TR=2000 ms
slices=35
dt (inter slice time) =TR/slices = 57,1428 ms.
Then, the 1
by
Karelo
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AFNI Message Board
Dear AFNI experts,
I have two datasets with a different acquisition slice order (tpattern). I would like to make sure that the slice timing correction with 3dTshift is well done.
1. First dataset.
TR=2 seconds
number of slices=35
slice order= Interleaved (1,3,5,7...35; 2,4,6,8...34).
Command used:
3dTshift -tpattern Alt+z -Fourier -prefix s_001_stc.nii s_001.nii
2. Secon
by
Karelo
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AFNI Message Board
Dear AFNI experts,
I have two datasets with a different acquisition slice order (tpattern). I would like to make sure that the slice timing correction with 3dTshift is well done.
1. First dataset.
TR=2 seconds
number of slices=35
slice order= Interleaved (1,3,5,7...35; 2,4,6,8...34).
Command used:
3dTshift -tpattern Alt+z -Fourier -prefix s_001_stc.nii s_001.nii
2. Se
by
Karelo
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AFNI Message Board
Dear AFNI experts,
I am wonder what is the difference between these two examples of censor motion using 1d_too.py.
What is different when you use '-censor_motion' or '-moderate_mask'?
a. general example ~3~
1d_tool.py -infile motion.1D -set_nruns 9 \
-derivative -censor_prev_TR \
-collapse_cols
by
Karelo
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AFNI Message Board
Dear AFNI experts,
I am using 3dTproject to do nuisance regression to my data. We are using the -censor option to mitigate the effect of outliers time points. Sometimes, I have got the following error:
ERROR_message "run #%d has only %d points after censoring need at least %d;
After a few tests I found that the program shows this error when the censor file have more than 25.9 %
by
Karelo
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AFNI Message Board
Dear AFNI experts,
I am using 3dTproject to do nuisance regression to my data. We are using the -censor option to mitigate the effect of outliers time points. Sometimes, I have got the following error:
ERROR_message "run #%d has only %d points after censoring need at least %d;
After a few tests I found that the program shows this error when the censor file have more than 25.9 %
by
Karelo
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AFNI Message Board
Gang,
> Could you describe the types of those explanatory variables (including covariates)? Are they between-subject or within-subject?
We will perform two analyses. The first one include 7 within variables of interest (3 main effects and the 4 possible interactions) , 2 covariates of no interest (within) and 2 factors of no interest (between). The second one will include 2 variables of
by
Karelo
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AFNI Message Board
Dear AFNI experts:
Is it possible to run AFNI group analysis related functions (3dttest++, 3dANOVA, 3dLMEr) using surfaces instead of volumetric data?
If so, I am interested to do a multiple regression with the following variables:
- Dependent variable = the surface.
- Independent variables/regressors = 7 physiological measures (3 main effects and 4 interaction effects).
- 4 covariates.
by
Karelo
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AFNI Message Board
Dear AFNI experts,
After reading the documentation and message board about different
approaches for movement correction/mitigation (including concepts and
calculations) I still have some questions:
1. If I apply enorm censoring, would it be reasonable to also regress
the 6 motion parameters and it's derivatives at the subject level? The
question arises because both options (enorm a
by
Karelo
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AFNI Message Board
Hi Rick,
Thank you so much for your reply. I had been talking with Bob about this topic, and the problem was more specific than I thought. Even though the problem is solved, I would like to post what happened because this could be useful for other users.
Basically, I was trying to use "sub bands" which are bands with very short frequency ranges. The cause of the error in the pro
by
Karelo
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AFNI Message Board
Dear AFNI experts,
I am using 3dTproject to do nuisance regression. Sometimes we combine different fixed of regressors (movement parameters, physiological recordings, etc.) and also a band pass filter.
The problem appears when I try to band pass at "0.002 - 0.01" or "0.012 - 0.028" Hz combined with the mentioned fixed regressors.
It seems that band passing at those fre
by
Karelo
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AFNI Message Board
Dear AFNI experts,
I am using 3dTproject to do nuisance regression. Sometimes we combine different types of regressors (movement parameters, physiological recordings, etc.) and also a band pass filter. The problem appears when I try to band pass at "0.002 - 0.01" and "0.012 - 0.028".
It seems that band passing at those frequency ranges use at least more than 90% of the D
by
Karelo
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AFNI Message Board
I would also like to ask the following question:
I am interested to compare results between two samples. In the first sample nuisance regression was done by using fixed regressors (movement, physiological recording, white matter, etc.) and a band pass filter in a certain frequency range. On the other hand, in the second sample nuisance regression was done by using only the band pass filter.
by
Karelo
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AFNI Message Board
Dear AFNI experts,
I am using 3dTproject to do nuisance regression. Sometimes we combine different types of regressors (movement parameters, physiological recordings, etc.) and also a band pass filter. The problem appears when I try to band pass at "0.002 - 0.01" and "0.012 - 0.028".
It seems that band passing at those frequency ranges use at least more than 90% of the D.
by
Karelo
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AFNI Message Board
Dear AFNI experts,
I previously detrended an EPI with 3dTproject without the band pass filter option. Now, I am interested in calculating ALFF and fALFF with 3dRSFC.
Is it correct to use the band pass option in 3dRSFC in order to calculate fALFF denominator considering that the input EPI was previously detrended?
Thanks in advance,
Karel
by
Karelo
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AFNI Message Board
That make sense. Thank you so much Robert.
Best regards,
Karel
by
Karelo
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AFNI Message Board
Dear AFNI team,
I am working with small ROIs and I am interested to smooth the data within the limit of a specific mask. The problem is that the majority of these masks have less than 333 voxels, which means that the program will show the error "Mask is too small to process".
I found the source code of the function in GitHub and the line in which I could modify the value (limit amo
by
Karelo
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AFNI Message Board
Thank you so much Daniel. It worked with -cost lpc+ZZ.
Best regards,
Karel
by
Karelo
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AFNI Message Board
Dear AFNI team,
I am doing registration between EPI images and its T1. The registration is almost perfect in all subject except in one (73 of 74 subjects). I would like to attach the code that I am using to perform the registration.
align_epi_anat.py -anat T1 \
-epi EPI \
-epi_base BASE_VOLUME \
-epi2anat \
-suffix _pre.nii \
-anat_has_skull no \
-epi_strip 3dAutomask \
-v
by
Karelo
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AFNI Message Board
Hi Paul,
Thank you so much! It was very helpful.
Best regards,
Karel
by
Karelo
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AFNI Message Board
Dear AFNI group,
I am wonder how the mentioned program performs the calculation. As long as I know using 3dTproject without -bandpass option will dentrend the signal by a regression using provided vectors and a polynomial order. But, if I use -bandpass option, will the program do the same as above and then filter the frequency? or it applies the filter first and then the regression?
Thanks
by
Karelo
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AFNI Message Board
Dear AFNI experts,
We realized that we have voxels outsite of the brain with very low values (e.i. 0.0867) after we run:
3dAllineate -prefix output.nii -base MNI_template -source Image -1Dmatrix_save file_aff12.1D
Then, after using 3dQwarp, these low values extend even further. We run the command in the following way:
3dQwarp -prefix output_Qwarp.nii -base MNI_template -source
by
Karelo
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AFNI Message Board
Dear AFNI experts,
I am interested to know if is possible to install AFNI in the new Ubuntu 19. I did not try it yet. I am just wondering if updating my System.will be worth it in term of installing softwares.
Best regards,
Karel
by
Karelo
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AFNI Message Board
Dear AFNI experts,
I am using Dimon to convert DICOMS to nifti. I normally use the following code to convert Phillips DICOMs.
Dimon -infile_pattern 'IM_*' -GERT_Reco -quit -use_last_elem -use_slice_loc -dicom_org -sort_by_acq_time -gert_write_as_nifti
For some reason I am having issues with this subject in particular and I am not sure about the cause of that.
Could someone
by
Karelo
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AFNI Message Board
Dear AFNI experts,
I am interested to know what could be the best approach to control physiological artifacts (respiration and pulse) without physiological records during the fMRI session. I am trying to use 3dDetrend or 3dTproject with higher order polynomials to control those low frequency signals. But, I read in a lot of papers that filtering (bandpass) can handle this situation very well.
by
Karelo
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AFNI Message Board
Hi Rick,
Thanks for the recommendations. I think there is not a problem with DICOM files in this case. Indeed, the information is the same if I compare the runs which did not have the motion problem with the ones with the motion problem. What can I do to handle this issue? I know that motion in general is a real problem and evidence shows that it can be mitigated until some point (doing alignm
by
Karelo
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AFNI Message Board
Hi Rick,
Thank so much for the answer, it makes a lot of sense. Everything indicates that there is a high probability to be a scanner issue.
The scanner is a local one (the one in our University; Phillips Ingenia 3.0) and the data is still being acquired. In your opinion, what could be the best solution to handle this situation? Should we ask for technical support? Or is there a special way
by
Karelo
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AFNI Message Board
Hi Rick,
If I look at the time series of one of those runs without any preprocessing, when I pick one voxel within the brain sometimes it looks relatively fine (without spikes). But, if I pick a voxel near to de edge of the the signal it looks very similar to that motion parameter (see image as an example). I also attached a gif showing a video of the time series in which you will notice an ab
by
Karelo
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AFNI Message Board
Dear AFNI experts,
We are analyzing a task-based experiment at individual level. The task contains 7 runs. When we look at the movement parameters in each run, we have noticed that in some of these runs the dP parameter contains spikes followed by squared and flat waves (see the attached figures). For some unknown reason, this component of motion is not modeled correctly. Which could be the ca
by
Karelo
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AFNI Message Board
Thank you so much Gang! after clarifying the inaccurate term "eliminating", the main idea is starting to make sense for me.
by
Karelo
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AFNI Message Board
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