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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: 123
Results 31 - 60 of 75
Hi,
I am using the dataset#N plugin to overlay several time series in the graph. When I launched several AFNI windows locked to each other, the setting of dataset#N seems to apply to every AFNI window. I am wondering if there is a way to set different dataset#N combinations for different windows?
Thanks!
Mingbo
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Mingbo
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AFNI Message Board
Hi Gang,
Thanks for the reply. I just realized that I can use '\' to indicate different rows in gltsym.
Sorry there is one more question:
For specifying lag of one stimulus, if I use CSPLINzero(0,12,5) , does the first coefficient after the zero starting point (the one at delay 3 sec) counts as lag 0 or lag 1?
Mingbo
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Mingbo
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AFNI Message Board
Thanks Gang!
For the last question, can I understand it in this way: as long as all possible linear combination of all rows can cover any contrast of any two conditions, and these rows are orthogonal to each other, then the f-statistics is fine?
For example, if I have 4 levels, then a matrix as follows would be equivalent to an ANOVA on individual level, right?
1 -1 0 0
0 1 -1 0
0 0 1 -1
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Mingbo
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AFNI Message Board
Hi,
I am trying to understand how the glt works in 3dDeconvolve on individual level. Say I am contrasting two conditions, is the p-value based on the estimated beta of the two condition and the estimated standard deviation of the betas?
More specific questions based on this:
If I want to test whether :
(1) condition A is bigger than condition B AND condition A is bigger than condition C
(2
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Mingbo
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AFNI Message Board
Hi Rick,
Thanks! That is a good way to work around. I was also wondering how to expand the number of orthogonal signals? It makes sense for most users to put motion parameter or physiological signals to reduce noise and 1 orthogonal signal is probably not enough. I tried to modify the model_linplusort.c but it gave me errors of not able to inverse matrix or something like that yesterday.
Ming
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Mingbo
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AFNI Message Board
I kind of figured out how to input the ort signal. However it does only allow one time series. In practice I think it would be very useful to include more orthogonal time series (e.g., principal component in CSF or motion parameter). Can someone teach me how to expand the number of orthogonal time series allowed?
The censor is still quite important to me. Is it possible to expand 3dNLfim to in
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Mingbo
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AFNI Message Board
Hi,
I have not found this in the documentation. I am wondering how to censor certain TRs in 3dNLfim as is done in 3dDeconvolve?
Another question is, for the linear+ort model, the code seems to describe the third baseline model as quadratic trend. But from the name I thought this is supposed to be some user defined signal to be regressed out (such as motion or physiological signal). Can someon
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Mingbo
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AFNI Message Board
I had just the opposite problem: for some of my subjects the 3dSkullStrip cuts too much around the pre- and post-central gyrus. And after I warp the EPI to the template (I was using the MNI template shipped with FSL since that one is less blurred than the version shipped with AFNI), that part turns to protrude outside the brain. However I found that by now freesurfer gives me the best skull-strip
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Mingbo
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AFNI Message Board
Hi Daniel,
Thanks. That explained it. I was using sub-brick selector. I will do the 3dcalc trick. But it would be good if it at least appends the history of 3dclust itself so that the clipping threshold etc. are saved.
Mingbo
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Mingbo
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AFNI Message Board
Dear AFNI fellow,
Would you mind making 3dclust append the command to the output mask's history when using -savemask? Currently it even swipe out the history of the file used for generating mask.
Thanks!
Mingbo Cai
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Mingbo
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AFNI Message Board
Thanks! I am not using GIFTI. Then I will go ahead and update everything.
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Mingbo
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AFNI Message Board
Hi Ziad,
I am still a bit confused. I found strange that although I run every subject with the default recon-all command in freesurfer, some of them I can run through @SUMA_Make_Spec_FS with the default option, some of them I have to provide -use_mgz in order to get it to run. The output with only -sid option will give the following output:
-- found 6 LH surfaces
-- found 6 RH surfaces
echo
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Mingbo
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AFNI Message Board
Thanks Ziad,
I somehow thought I have to use one option among them.
Mingbo
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Mingbo
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AFNI Message Board
Hi, In the @SUMA_Make_Spec_FS command, there is an option of -use_mgz and an option- nocor. I do not really understand the difference between them. -nocor seems not working so I just chose -use_mgz. But I am curious if there is any pros/cons of using one vs. the other?
Thanks!
Mingbo
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Mingbo
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AFNI Message Board
Oh, I think I know what was wrong. In Matlab, the scale parameter is in the denominator, but in the cdf package AFNI uses, it is in the numerator.
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Mingbo
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AFNI Message Board
Hi Issac and Gang,
I was able to save the file. But the p-value I see was bizarre in AFNI. The inverse cumulative probability function of my Gamma of 0.95 (which I think means anything above this is in the top 5% range of possible value in the Gamma distribution) is around 2.69. But when I drag the threshold bar around this value, the p-value AFNI shows is very large, like 0.92. (I am sure the d
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Mingbo
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AFNI Message Board
Thanks Isaac,
Just out of curiosity, what does FUNC_PAIR_TYPE or FUNC_THR_TYPE means?
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Mingbo
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AFNI Message Board
Thanks Gang and Isaac,
The data I processed in AFNI is actually read from BRIK file, so at least I have a basic header structure in Matlab to modify with.
So here is the situation: assuming I have data of different conditions. A null model assumes that for any voxel, each condition gives the same response, and the deviation of signal observed from the estimated average response is just noise
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Mingbo
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AFNI Message Board
Hi,
I am not very familiar with all the tags in the header file. If I have used Matlab to generated some parameter (say, of the tuning curve of each voxel), and some value (say, the percentage of variance my tuning curve can explain for each voxel) that I want to use as threshold to visualize in AFNI, how should I assign those header info to these two types of data when I write data to BRIK file
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Mingbo
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AFNI Message Board
Ha Nick, I mistakenly thought it was Bob responding to my last post. How do you feel about the python package?
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Mingbo
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AFNI Message Board
Thanks Rick, what I were hoping was the one Bob pointed out. In the way you suggested, I would get the same amplitude response for all condition. But it is possible that they may have the same shape but different amplitude. This gives more constraint compared to fit TENT function for each individual condition. But perhaps for now, the python package and some matlab function is OK. I am going to s
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Mingbo
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AFNI Message Board
Thanks Bob,
I think this is exactly what I want. This will be useful for encoding and decoding. My assumption is that HRF can vary between voxels, but for individual voxel, HRF shape is more likely to be fixed with beta varies between conditions. I am currently fitting this with least squared error fitting in Matlab, with the assumption that temporal noise is i.i.d. But I would hope AFNI has som
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Mingbo
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AFNI Message Board
Hi,
I am wondering what is the best command to deconvolve the signal to different conditions, but assuming they share the same hemodynamic response function. It is similar to IM, allowing HRF to vary between voxels (fixed for each voxel), but estimating beta only for each condition, instead of for each trial.
Thanks!
Mingbo
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Mingbo
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AFNI Message Board
Hi,
I noticed that when applying the same align_epi_anat.py command to different data sets, sometimes there is a transformation file writen with suffix like _e2a_only_mat.aff12.1D, sometimes it is _mat.aff12.1D. The prefix is usually the name of the anatomic data.
I think they are the ones used when warping the anatomic data to match epi data with 3dAllineate -1Dmatrix_apply. But I am just cur
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Mingbo
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AFNI Message Board
Hi Bob,
Thanks! That is a very interesting idea. I read their protocol a bit but did not realize they were doing in this way. I agree with you that the field map result is semi-reasonable. For some parts it seems to make the EPI match structure better, but for some other parts it can over compensate (if I am not doing things wrong) and the performance seems to vary with subjects.
I will give
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Mingbo
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AFNI Message Board
As a side note, has anyone used the 3dQwarp between EPI and structure? What would be the best way to use?
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Mingbo
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AFNI Message Board
Hi all,
I had been searching for a way to use the field map correction of FSL and transform back to AFNI with the minimum steps of interpolation. The threads on the forum about this seemed not complete. And the major problem I encountered is the coordinate seems to be messed up after bringing FSL result back to AFNI (especially if I want to align epis of multiple sessions to a common structure).
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Mingbo
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AFNI Message Board
Hi Daniel,
Thanks for the suggestion. I chopped two top slices (one includes only a few voxels of brain) and compared align_epi_anat.py (with rigid body transform) and 3dvolreg.
align_epi_anat.py generates the same alignment for mapping original epi to an anatomy vs mapping a chopped version of the same epi to the same anatomy.
However, 3dvolreg does generate slight different alignment when al
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Mingbo
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AFNI Message Board
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Pages: 123