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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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Ok I found a solution: Creating a file /.Rprofile in the user home directory with the line xinit = "NA" solves the issue, which is probably only showing up under WSL2 which contains some changes about xserver compared to WSL1.
However, I receive now an unrelated error:
Error in inData : no 'dimnames' attribute for array
Execution halted
Probably because I use nifti
by
paranoidandroid
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AFNI Message Board
Hi,
I am trying to run 3dLMEr under WSL2 (running ubuntu 20.04).
I made sure I installed all the R packages.
I set up everything according to the manual and the AFNI GUI opens without problems.
But the problem seems to be related to the the xserver, "object xinit not found" happening inside R.
Could it be missing some global variable? or do I have to modify some R settings?
App
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paranoidandroid
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AFNI Message Board
rick reynolds Wrote:
-------------------------------------------------------
> What program was used in AFNI? It certainly
> looks
> like the AFNI program was not informed of the
> expected BOLD response.
>
> Presumably you want to detrend in the context of
> a
> linear regression, where the estimated BOLD
> response
> is included in the model. Is that
by
paranoidandroid
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AFNI Message Board
Hi, Sorry for bringing up this very old thread, but I have a related problem, for which I couldn't find a solution with AFNI:
If you have a scan with very strong and prolonged BOLD response (e.g. pharmacological fMRI), you wouldn't want your detrending polynomial to be based on all datapoints.
E.g:
The blue line is the correct detrending line, (here with matlab, which allows exc
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paranoidandroid
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AFNI Message Board
Hello,
I've been using 3dNLfim quite a lot, and the number one feature I miss is the -CENSORTR option as in 3dDeconvolve to ignore time points with artifacts.
There is already the option -ignore but it only skips the initial images from analysis. Would be great if one could add more time points under this option separated by comma as with censortr.
Thanks a lot if you can find the t
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paranoidandroid
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AFNI Message Board
Yes, basically I want the HRF, which was fitted to the data not from a stimulus time series (zeros and ones) but from the neuronal signal that has some continuous value at every time point.
-stim_times_AM2 might be exactly what I want, if I define every single time point as stimulus event which is amplitude modulated by the neuronal signal. Will try...
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paranoidandroid
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AFNI Message Board
I would like to enter a regressor that represents the neuronal activity (acquired with electrophysiology), therefore. a hemodynamic response function should be fitted to it.
It is a time series with the same duration as the fMRI scan consisting of continuous values.
I can't find a way to do it in 3dDeconvolve: -stim_times is expecting onset times in seconds. -stim_file would accept a
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paranoidandroid
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AFNI Message Board
Problem solved, thanks for the idea with the filesize.
The file was 184320600 bytes, leaving only 592 unexplainable bytes. It turned out the labview software added 8 bytes for every frame, so (1280*960*2+8)*75=184320600.
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paranoidandroid
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AFNI Message Board
I am trying to convert a binary file containing a series of images (intrinsic imaging data) into BRIK format.
using the following code, I get a reasonable image for the first timepoint:
to3d -fim -view orig -prefix test -time:zt 1 75 200 zero -xFOV 10L-R -yFOV 10A-P -zFOV 0S-I 3Ds:8:0:1280:960:75:file
(i.e. the file has 75 images with 1280x960 pixels and 200ms resolution, I dont know the ex
by
paranoidandroid
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AFNI Message Board
actually I wanted to use it as a way to downsample the data to a certain nonisotropic voxel size.
I guess I can achieve the same thing with 3dresample then.
But I still think it would be a useful feature to have independent x,y,z FHWM values for blurring, although I cant think of a good example right now...
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paranoidandroid
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AFNI Message Board
I would like to smooth a dataset with different FWHM values for x,y,z. say 2mm in x, 3mm in y etc.
Unfortunately I could not find a way to enter more than one number in 3dmerge or 3dBlurToFWHM. Forum search revealed a tool called 3dnonisosmooth, but it does not seem to allow this either, at least the help does not say how to enter FWHM values as parameters...
Am I missing something, or is there
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paranoidandroid
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AFNI Message Board
In 1d_tool.py when using the option -censor_motion, it outputs this nice motion_enorm.1D file with the combined 6 motion vectors.
However, I found no way to recreate this file for the -weighted_enorm option.
This would be extremely useful to calibrate the -weight_vec values and see how much it affects the result when collapsing the columns.
It's certainly caluclated somewhere to produce t
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paranoidandroid
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AFNI Message Board
Just for clarification, if one would want to use the full shape information for the group analysis.
you would take the -iresp outputs and run 3dDeconvolve again for every subject? (because unfortunately i dont think -iresp comes with a b and t- value).
Or how about using the -fitts time series?
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paranoidandroid
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AFNI Message Board
I've been working with mouse data (but not resting state) for quite some time and unfortunately there is no standard brain, and we were not very successful with coregistering to T1 images. There may simply be not enough structure in the mouse brain (no sulci, gyri like in the human brain) to make meaningful transformations.
Although, I think some resting state people have been claiming to c
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paranoidandroid
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AFNI Message Board
Thanks a lot, this niml.dset format works great.
one last remark: to open it e.g. in matlab it has to be converted with "ConvertDset -o_niml_asc data.niml.dset"
by
paranoidandroid
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AFNI Message Board
Hi,
I would like to adapt this standard data scaling code to a dataset that has
multiple rows with one row for each voxel, and multiple columns representing the time axis.
3dcalc -a dataset.1D -b mean.1D \
-expr 'min(200, a/b*100)*step(a)*step(b)' \
-prefix dataset.scaled
Unfortunately, I could not find a way to trick 3dcalc to treat these files as voxel time series an
by
paranoidandroid
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AFNI Message Board
Apparently 2dImReg requires square slices.
What can I do to realign 2D slices with rectangular slices? I tried 3dQwarp or 3dWarpDrive with varying error messages...
Also the trick with 3dZeropad doesn't work since the FOV and voxel sizes are so unfortunately chosen that there is no integer solution for adding zero-voxels to make the images square.
by
paranoidandroid
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AFNI Message Board
once, again thank you rick,
It works now, but its very demanding with the inputs:
if anyone wants to try this in the future (with my files provided above), this is the syntax:
3dConvolve -input zeros_template+orig -polort -1 -num_stimts 1 -stim_maxlag 1 20 -stim_file 1 4blocks_zeros_ones_for_convolution.1D -iresp 1 mean_iso_HRF+orig -output Ideal_Block_Model
(the IRFs have 21 time
by
paranoidandroid
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AFNI Message Board
Dear Afni Experts,
I want to do a very simple convolution, using 3dConvolve.
This is the command:
3dConvolve -input mean_iso_HRF+orig -num_stimts 1 -stim_file 1 4blocks_zeros_ones_for_convolution.1D -output Ideal_Block_Model
the input is a 3d+time dataset containing the hemodynamic response functions, the stim file is a simple column vector.
Below are the files involved, maybe it is of
by
paranoidandroid
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AFNI Message Board
This is basically a continuation of this thread:
But my questions are more general. As far as I understand the only reasonable way to perform a group analysis of 3dNLfim statistical outputs is to do a multivariate test with 3dMVM. It wouldn't make sense to put all the parameters of a nonlinear equation (a^b-c or something) in an ANOVA model where they would be incorrectly modeled (as y=
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paranoidandroid
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AFNI Message Board
Gang Wrote:
> No, 3dMEMA does not allow for multiple inputs from
> each subject. So the results from 3dMVM are not
> powerful enough?
I just get too many false positive voxels with 3dMVM, the correct regions are detected but also a lot of other stuff, in particular at the border of the brain, and thresholding doesn't clean it up.
The reason is most likely that these voxels h
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paranoidandroid
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AFNI Message Board
> Good to know! Did you run 3dMEMA on each parameter
> separately?
Hi Gang, is there a way to run 3dMEMA on multiple parameters and get an F-statistic?
So far I did it like example1 of the help, run it separately for each pair of Coef&Tstat .
Do do a kind of ANOVA, should I construct two BRIK files for each subject containing the corresponding coefficients and Tstatistics
by
paranoidandroid
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AFNI Message Board
I fitted some data (20s stimulus) using the SPMG3(20) model and got results like the one shown below (fit in blue):
Are there no constraints on the combinations of the basis functions? I am just wondering how this peculiar shape with the 3 peaks can happen, it seems like an overfitting problem.
My goal is anyway to show that this model performs poorly for this particular data compared to
by
paranoidandroid
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AFNI Message Board
Ok, this might be a trivial problem, but I tried everything and cannot achieve the following with plugout_drive:
1. open an image window in controller A for directory (X).
2. open a new afni controller B.
3. open another image window in controller B for a file that is in a completely different directory (Y).
what I tried:
"SET_SESSION" or "SWITCH_DIRECTORY" do not wor
by
paranoidandroid
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AFNI Message Board
It works great now.
Unfortunately I seem to have too few subjects for multivariate analysis (I still dont quite get how degrees of freedom are obtained), eventually I would have 4 groups with ~6 subjects each.
However, I am getting excellent group results with 3dMEMA, it seems the incoroporation of the t-maps helps a lot with small groups...
by
paranoidandroid
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AFNI Message Board
I use the openmp_64 package.
the command is simply : 3dLRflip -LR input+orig
But anyways, the problem is reasonably solved: " 3dLRflip -LR -prefix flipped input+orig" works perfectly fine.
Without defining a -prefix it tries to create a weird filename by itself, at least considered by my language settings or something....
by
paranoidandroid
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AFNI Message Board
when I try to flip any file with 3dLRflip (AFNI version=AFNI_2011_12_21_1014 (Jan 8 2014) [64-bit])
I get this message:
++ processing input+orig ...
*** ERROR: failed to open file ./input_Lf Q\ufffd,*+orig.HEAD for attribute writing;
- Do you have permission to write to this disk?
- Is the disk full?
*** Datablock write error: failure to write attributes - is disk
by
paranoidandroid
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AFNI Message Board
ok, I uploaded two more scans to the folder.
Thanks a lot!
by
paranoidandroid
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AFNI Message Board
Dear Gang,
I uploaded the files here https://skydrive.live.com/redir?resid=4C8D30C2AD5C97AE!323&authkey=!AKCtcesUaV0l-Oc&ithint=folder%2c.HEAD
Are 6 subjects enough? Because the additional ones I added from another (wrong) group just as a proof of principle...
by
paranoidandroid
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AFNI Message Board
Thanks, this was the mistake. But then I get
Error in linearHypothesis.mlm(mod, hyp.matrix, SSPE = SSPE, ...) :
The error SSP matrix is apparently of deficient rank = 0 < 7
Calls: Anova ... Anova.III.mlm -> linearHypothesis -> linearHypothesis.mlm
Execution halted
I thoughts its because I have too few subjects, but even with 14 subjects the error remains...
EDIT: As yo
by
paranoidandroid
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AFNI Message Board
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