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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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Dear experts,
When I coregistered a result map to T1, the information in the 'statpar' field was lost and I need it to continue with other steps. Is there any way to perform the coregistration without losing this information?
Thank you in advance.
Best regards,
Marina
by
Marina Fernandez Alvarez
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AFNI Message Board
Dear experts,
We perform resting state preprocessing in volume until nuisance regression step included. After this, we perform surface analysis to calculate FC. Now, we are going to start task-fMRI experiments and we would like to know what is the recommended moment to project from volume to surface in a task-fMRI pipeline.
On the other hand, is it possible to unlink the first level analys
by
Marina Fernandez Alvarez
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AFNI Message Board
Dear experts,
I would like to perform a regression to find the signal amplitudes (betas) of the task model components while at the same time removing the nuisance model components with 3dREMLfit. In order to do that, how do I have to enter the onsets of the task?
Best regards,
Marina
by
Marina Fernandez Alvarez
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AFNI Message Board
Hi Daniel,
Thank you very much for you reply.
I tried to run the unWarpEPI.py function, but I saw that internally it uses 3dUnifize and I wanted to avoid using it. On the other hand, we do our preprocessing with AFNI in steps but without using the afni_proc.py function, so this would make it difficult to use the flags that this function has to make the correction with an inverted PE-EPI (-bl
by
Marina Fernandez Alvarez
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AFNI Message Board
Dear experts,
I would like to correct susceptibility artifacts of the EPI sequence with an inverted phace enconding (PE) EPI sequence that was acquired using the same parameters than the EPI but with inverse phase-encoding directions (P-A and A-P respectively). In order to perform this correction, I want to use 3dQwarp with –plusminus flag and 3dNwarpApply but I have some doubts that I hope yo
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Marina Fernandez Alvarez
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AFNI Message Board
Doubts solved! Thank you so much for the recommendations Daniel.
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Marina Fernandez Alvarez
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AFNI Message Board
Thank you for your reply Daniel.
I should clarify that the EPI volumes don’t have severe or evident artefacts and the reason why we would like to correct the inhomogeneities is to improve us much is possible the alignment of the EPI volumes. Considering these facts:
1) Do you recommend to apply 3dUnifize only in the case that the inhomogeneities are evidents?
2) In case that you think we s
by
Marina Fernandez Alvarez
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AFNI Message Board
Dear experts,
I would like to correct the inhomogeneities caused by spatial intensity variations in EPI volumes (as performs the “fast” function in FSL).
Is there an equivalent function in AFNI to do this?
Thank you very much in advance.
Marina.
by
Marina Fernandez Alvarez
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AFNI Message Board
Dear AFNI experts.
I have a question related to the 3dRSFC function. f/ALFF is defined as the power within a low-frequency range (for example: 0.01-0.1 Hz) divided by the total power. How does the function calculate the total power used as the denominator to calculate fALFF?
I would like to know if the function internally uses the option fbot=0 and ftop=9999 to get the total power of the fu
by
Marina Fernandez Alvarez
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AFNI Message Board
Perfect!
Thank you very much for the help, Paul.
Best regards,
Marina
by
Marina Fernandez Alvarez
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AFNI Message Board
Hi Paul,
Thank you very much for the information!
Now we are using the Freesurfer surfaces and I would like to implement that function. In addition, we are also interested in using SUMA for certain analyzes.
So how should I treat my freesurfer surfaces to use AFNI/SUMA functions?
If I have to transform them to gifti, what is the most correct way?
Thank you very much in advance.
B
by
Marina Fernandez Alvarez
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AFNI Message Board
Dear AFNI experts,
I would like to use a function to convert the x, y, z MNI152 coordinates into the vertex index of a surface.
Do you know any function that can give me the vertex index which corresponds to certain coordinates as output?
Thank you very much in advance.
Best regards,
Marina
by
Marina Fernandez Alvarez
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AFNI Message Board
Dear experts,
I would like to run a functional connectivity ROI-to-ROI analysis with AFNI (first level analysis).
First, I would extract the mean value of the seed-ROI in each subject.
Then, I would calculate FC between these seed-ROI values and the 250 EPI volumes masked by the target-ROI.
Should I use the 250 EPI volumes that are masked by the target-ROI with smoothing?
Or is it bett
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Marina Fernandez Alvarez
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AFNI Message Board
Okay Rick! Thank you very much for solving all the doubts!
Best wishes,
Marina.
by
Marina Fernandez Alvarez
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AFNI Message Board
Hi Rick,
Thank you very much for your reply!
> My guess is that you want srms, as it must be in [0,1]. But maybe there is a different scalar that you want, which would also
> scale into the 0.5 threshold. There is currently no method to apply this in afni_proc.py, as those curves seemed to noisy to
> be robust. But if it is something you feel is important, I could consider add
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Marina Fernandez Alvarez
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AFNI Message Board
Dear AFNI experts,
I'm sorry for asking again. Is it possible to calculate with AFNI the censor file of dvars values using a threshold of 0.5?
Furthermore, I would like to know what is the output that I can use as a regressor in the linear regression step, both in the case of enorm and in the case of dvars (if it is possible).
Any help is welcome! :)
Cheers,
Marina.
&g
by
Marina Fernandez Alvarez
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AFNI Message Board
Hi AFNI experts,
I would like to calculate dvars and use a threshold of 0.5% to generate the censor file which contains 1s (indicating time points to be included) and 0s (indicating time points to be excluded). In order to calculate dvars, I run the following command:
3dTto1D -input s_1_fMRI.nii -mask mask_s1.nii -method dvars -prefix s1_dvars.1D
I saw that the values of the output are
by
Marina Fernandez Alvarez
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AFNI Message Board
Dear AFNI experts,
I would like to smooth connectivity maps from the same dataset before the statistical analysis. Should I use 3dBlurToFWHM? Or do you recommend another function?
And what should I do if the images are from different datasets?
Thank you in advance.
Best regards,
Marina.
by
Marina Fernandez Alvarez
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AFNI Message Board
Hi experts,
I have projected 4D-AFNI preprocessed BOLD data to Freesurfer cortical surfaces. Resulting individual surfaces have many holes (see attached image) that I would like to fill with nearest neighbors values around each hole (avoiding the medial wall). Could you indicate me how to do this?
Thank you in advance.
Marina
by
Marina Fernandez Alvarez
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AFNI Message Board
Thank you very much for your reply.
I think I didn't explain the question well. The real question is whether when doing a voxel-wise analysis (or PET or fMRI, not both in the same analysis) it is mandatory to introduce the ICV as a covariate of no interest in the statistical model (as in VBM studies , which is mandatory).
For example, if you want to compare the voxel-wise differences o
by
Marina Fernandez Alvarez
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AFNI Message Board
Hi experts,
In 2nd level analysis, in which I use images from fMRI studies (for example, connectivity maps) and static PET images, should I add the ICV as a covariate?
Thank you very much in advance.
Best regards,
Marina.
by
Marina Fernandez Alvarez
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AFNI Message Board
Dear experts,
Should I apply the bandpass flag with 3dTproject? In the preprocessing I did retroicor and I am going to use the physiological variables in the nuisance regression (with 3dTproject).
In that case, should I apply it always (for resting state and task-related fMRI)?
What is the lowpass and highpass filter that you recommend me?
Thank you very much in advance.
Best rega
by
Marina Fernandez Alvarez
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AFNI Message Board
Thank you very much for the help, it was very useful.
Best wishes,
Marina.
by
Marina Fernandez Alvarez
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AFNI Message Board
Hi experts,
I would like to know when I should apply retroicor in the preprocessing of fMRI data (before and after which steps).
Is it correct to apply it after the motion correction and before the slice timing?
Thank you very much in advance.
Marina.
by
Marina Fernandez Alvarez
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AFNI Message Board