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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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Thank you Rick, I will try that and let you know any updates. I assume it will be useful for other M1 users.
Cesar
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Cesar Caballero Gaudes
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AFNI Message Board
Hello,
I'm having issues with R programs because R_io.so is not loading. I'm using a MacBook pro M1 Max and zsh.
Error in dyn.load(ll) :
unable to load shared object '/Users/ccg/abin/R_io.so':
dlopen(/Users/ccg/abin/R_io.so, 0x0006): tried: '/Users/ccg/abin/R_io.so' (mach-o file, but is an incompatible architecture (have (x86_64)
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Cesar Caballero Gaudes
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AFNI Message Board
Hello,
We want to convert statistical sub-bricks (t-stat) with different number of degrees of freedom using 3dcalc -expr 'fitt_t2z(a,z)'. Is there any command to obtain the statpar parameter in a batch? I could not find the obvious option:
3dinfo -statpar filename+tlrc
thank you in advance,
Cesar
by
Cesar Caballero Gaudes
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AFNI Message Board
Hi Rick,
Then, what's the actual command to shift the ideals in the FIM panel within the graph window?
Cesar
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Cesar Caballero Gaudes
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AFNI Message Board
Hi Daniel,
Thanks very much to you and Rick.
The following command did not work properly today.
❯ 3dTshift -linear -prefix newideal.1D -TR 1 -tzero 0 -tpattern '@1D: 1.2' mm_raw.1D\'
++ 3dTshift: AFNI version=AFNI_22.1.06 (Apr 24 2022) [64-bit]
** FATAL ERROR: Illegal value 1.2 in tpattern file 1D: 1.2
** Program compile date = Apr 24 2022
mm_raw.1D is the raw displace
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Cesar Caballero Gaudes
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AFNI Message Board
Hi Daniel,
I noticed that the suggested solution with subbrick selectors is valid for integer shifts of the time series, but the shift ideal option in the GUI also enables sub-integer shits (e.g., 0.5 steps). How is it possible to implement those?
Thanks in advance,
Cesar
by
Cesar Caballero Gaudes
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AFNI Message Board
Hello,
Is there any command to do the same as "Shift ideal" that is available in FIM -> Edit Ideal in the graph window?
Thanks very much,
Cesar
by
Cesar Caballero Gaudes
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AFNI Message Board
Hello AFNIers,
Let me tell you about an exciting event happening next week where AFNI users are really welcomed!!
The Basque Center on Cognition, Brain and Language (BCBL) is organizing the 3rd edition of Brainhack Donostia (https://brainhack-donostia.github.io), an event focused on neuroscience and the promotion of open-source resources in an accessible way across disciplines and experienc
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Cesar Caballero Gaudes
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AFNI Message Board
Hola Ana,
The error indicates that the number of nuisance regressors is larger than the number of time points after censoring. In other words, the remaining data would have -1 degrees of freedom!!
This is probably due to the combination of censoring and bandpass filtering. What is the TR of the acquisition? If the TR is too fast, bandpass filtering needs to include many, many regressors to
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Cesar Caballero Gaudes
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AFNI Message Board
Hello,
Let me jump in :)
Regarding point 3), I think 'Karelo' refers to the definition of 'srms' in 3dTto1D where srms = scaled rms = dvars/mean, and it is suggested that "SRMS survives both a resampling and scaling of the data. Since it is unchanged with any data scaling (unlike DVARS), values are comparable across subjects and studies." (taken from )
My
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Cesar Caballero Gaudes
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AFNI Message Board
Hello
I would say that 3dDeconvolve and 3dREMLfit would give you very similar beta values because the main difference between the two programs is regarding the modelling of the residuals. Therefore, if 3dREMLfit is very slow, I would use 3dDeconvolve.
Since the number of trials is relatively equivalent to the number of time points, you might have a look to 3dLSS that also estimates beta am
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Cesar Caballero Gaudes
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AFNI Message Board
Hello,
Similar to Paul's excellent recommendations, I think the most (probably unique) reasonable way is through the beta correlations, i.e. using the -stims_times_IM, that you also propose. However, it is not normal that the 3dDeconvolve command takes so long. Could you please post it? Alternatively, what's the dimensionality of the dataset(s), number of trials per condition, TR?
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Cesar Caballero Gaudes
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AFNI Message Board
Hi Daniel,
Yes, we are trying to fill holes based on neighbouring voxels, for instance a sphere but considering a mask within that region. And we don't want to take the average value as in 3dLocalstat, but would prefer some kind of high-order interpolation. They are floating point values.
Best,
Cesar
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Cesar Caballero Gaudes
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AFNI Message Board
Hi Daniel,
Thanks for the suggestions. One question: Does 3dAllineate have the option of setting a mask in the source image so that masked voxels are ignored for the interpolation? In fact, we want to fill in these voxels that we know shouldn't be zero.
We will try 3danisosmooth.
Best wishes,
Cesar
by
Cesar Caballero Gaudes
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AFNI Message Board
Hi Rick,
The point is that we are not doing any spatial transformation since the data is in the same space. I checked 3dresample but it does not have any option for mask.
As for 3dAllineate, is it possible to use it with no spatial transformation or how an identity transformation can be coded? Could the options -emask ee or -source_mask sss serve for our purposes? We only want to do the
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Cesar Caballero Gaudes
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AFNI Message Board
Dear AFNI friends,
I would like to interpolate the value of some voxels with zero values considering neighbouring voxels within an ROI (e.g. sphere, box) and that it can also consider a mask (e.g. tissue mask) to indicate which voxels to consider. Is there any program that can perform this beyond the options of 3dLocalstat? For instance considering a linear interpolation or high-order spline i
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Cesar Caballero Gaudes
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AFNI Message Board
you can apply 3dcalc to mask the phase image, for example as follows
3dcalc -a phase.nii -b mask.nii -expr 'a*b' -prefix phase_masked.nii
Hope this helps,
Cesar
by
Cesar Caballero Gaudes
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AFNI Message Board
Hello,
I am interested in computing a map of the local homogeneity of the time series, i.e. some kind of spatial correlation, within the voxel's neighbourhood.
I had a look to several programs such as 3dReHo (but it does not fit my purposes because it does rank ordering), 3dLocalStat (which is not appropriate for 3D+time dataset) or 3dLFCD (but it only returns the number of voxels exc
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Cesar Caballero Gaudes
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AFNI Message Board
Hello,
Yes, they are equivalent. The censoring regressors, where each only includes one value of 1 at the time point to censor and the rest of values to zero, can perfectly model signal at that time point. For instance, if the value of the time series is X, the weight of the corresponding censoring regressor will also be X so that the fit is perfect (i.e. no residual). In addition, "killi
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Cesar Caballero Gaudes
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AFNI Message Board
Hi Rick and Daniel,
Yes, Rick's solution is what I need. Thanks very much.
Best wishes,
Cesar
by
Cesar Caballero Gaudes
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AFNI Message Board
Hello,
I have generated simulated data (voxel time series) in the form of a 2D matrix ( N voxels x T timepoints). I would like to save it in a 3D+time dataset, for example a dataset with one slice (nx=ny and nz=1) and nt=T timepoints, in order to visualize it in AFNI. I've looked at 3dEmpty, but I am not sure whether it is the best option. Any suggestion?
Thanks in advance,
Cesar
by
Cesar Caballero Gaudes
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AFNI Message Board
Hello,
I think the option -tcat_remove_first_trs in afni_proc.py is what you are looking for
Best,
Cesar
by
Cesar Caballero Gaudes
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AFNI Message Board
Dear AFNIers,
Is there any program (o combination of programs) to compute a timeseries (.1D file) with the spatial correlation between a 3D+time dataset and a reference dataset? Or even more the spatio-temporal correlation if the reference dataset is also a 3D+time dataset with less bricks that defines an spatiotemporal pattern of interesting activity? This is to compute instants when a given
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Cesar Caballero Gaudes
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AFNI Message Board
Hi Rick,
I'm dealing with the same errors with the R packages in my Mac using macOS Mojave version 10.14.1
This is occurring in any attempt to use any R-based command, for example
cesars-MacBook-Pro:~ cesar$ rPkgsInstall -pkgs ALL
*** caught segfault ***
address 0x0, cause 'memory not mapped'
Traceback:
1: .Call("R_SUMA_HistString", ExecName, args, ohis
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Cesar Caballero Gaudes
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AFNI Message Board
Hello Afniers,
What's is the range of values of the figure generated with 3dGrayplot? Is it in signal percentage change, e.g. +/- 0.02?
Best
Cesar
by
Cesar Caballero Gaudes
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AFNI Message Board
Hi again,
The error appeared because one of the datasets had TR = 0, and using 3drefit -TR sorted it out.
Thanks,
Cesar
by
Cesar Caballero Gaudes
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AFNI Message Board
Hello,
I'm trying to run 3dTcorrelate with two datasets that have the same number of time points (215) according to 3dinfo -nt, but then 3dTcorrelate indicates that they don't have the same length. Here are the commands
>>> 3dTcorrelate -overwrite -pearson -Fisher -prefix TCORRmap.nii.gz P3SBJ01_Events01_MEICA_RHO0_BIC_SPMG1.dr2HRF_E02.nii.gz P3SBJ01_Events01_DN.FBrain
by
Cesar Caballero Gaudes
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AFNI Message Board
Is there any program to change the coordinate system of an affine transformation, for instance from LPI to RAS?
Thanks in advance,
Cesar
by
Cesar Caballero Gaudes
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AFNI Message Board
Page 1 of 3
Pages: 123