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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: 12345
Results 91 - 120 of 144
Here is the alias I am using (from now forward) for displaying bigger fonts in AFNI:
alias abig afni \
-XXXfontA \
-adobe-courier-bold-r-normal--25-180-100-100-m-150-iso8859-1 \
-XXXfontB \
-adobe-courier-bold-r-normal--20-140-100-100-m-110-iso8859-1 \
-XXXfontC \
-adobe-courier-bold-r-normal--20-120-100-100-m-100-iso8859-1 \
-XXXfontD \
-adobe-courier-b
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RWCox
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AFNI Message Board
The approach with 3 separate runs is more faithful to the modeling idea of finding differences between/among the varying stimuli. In the 1 big run approach, the separate stimuli that are glued together will get fit with 1 beta, except for the left-out individual stimulus. In the 3 run approach, the different stimuli (again, except the left-out one) will get 3 different betas, which should be slig
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RWCox
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AFNI Message Board
They are the smallest and largest t-statistics found in each iteration of the randomization.
In turn, they are used to compute the 'XX.5percent.txt' output file, which is the threshold to use for voxelwise thresholding at the 5 percent (and other percentiles) global FPR level. This threshold is usually pretty strict, which is why clusterwise thresholding was invented in the first pla
by
RWCox
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AFNI Message Board
You might want to try the '-lpa' cost function option when matching two datasets like this with similar contrast. That is, if the the original alignment isn't good enough.
by
RWCox
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AFNI Message Board
We can't answer your question, as we don't really know much about those other software tools you mention (GIFT, CONN, and REST). In particular, we don't know about how they compensate for movement or baseline drifts or other artifacts.
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RWCox
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AFNI Message Board
Since you do not have any stimulus timings, what do you mean here by "activations"? Inter-voxel or Inter-region correlations? How did you compute "activations" from the results of the afni_proc.py run?
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RWCox
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AFNI Message Board
I don't understand what you mean by this phrasing:
"non-stationary NOTMOCO and stationary data MOCO (MOCO has motion 0.1mm-0.3mm band and NOTMOCO has motion 1mm-2mm band and MOCO is the motion corrected NOTMOCO data created by MR own software)".
What does "motion xx-yy band" mean? What does "created by MR own software" mean?
In any case, setting the mot
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RWCox
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AFNI Message Board
When you say "many runs", how many is "many"? The reason I ask is that it sounds like each run has one movie-event only, and averaging across events is part of the usual FMRI analysis strategy.
The answer to your specific question depends on the question you are asking about the time series shape during the movie interval, versus the pre- and post-movie rest intervals. If a
by
RWCox
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AFNI Message Board
I can tell you WHAT this error is, but not how to fix it :(
3dDespike is written to use the OpenMP parallelizing system for speed -- that is, it runs in multiple threads. The binary version of AFNI you have installed must be compiled to use OpenMP using gcc. "libgomp" is "library gcc OpenMP" -- but that is not installed on your computer.
Fixing this requires either (a) u
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RWCox
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AFNI Message Board
You should use the newer program make_random_timing.py which has more options to control the timing.
by
RWCox
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AFNI Message Board
Q1: It does not make sense to use amplitude modulation with IM, since computing the coefficient (beta) for the AM component requires at least TWO events -- one for the beta describing the mean response, and one for the beta describing the variable response. With IM, there is only one event per regressor. Instead of AM, you get a different beta for each event time in the same stimulus file -- and
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RWCox
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AFNI Message Board
I'm pretty sure that the "illegal variable name" is the "$(2)" in your sub-brick selector "[0..$(2)]". Put this in 'single quotes' (and also change "[1..$(2)]" to '[1..$(2)]') and try again. The $subj is OK.
Inside "double quotes", the shell expands $variablename -- but you can't have a variable named '(2)
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RWCox
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AFNI Message Board
I don't have any such recommendations available. I did the command line addition to 3dTstat in an hour or so, after seeing the idea on Twitter. I added the GUI part a couple days later in an attempt to avoid doing something more important and less pleasant. But I don't have any experience in using MSSD or similar quantities for analyzing/interpreting brain data time series.
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RWCox
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AFNI Message Board
We take the skull image, and using the extremely stable processes of analytic continuation and sheaf cohomology on complex (holomorphic) manifolds, the skull bump map can be projected to the cortical surface, and then correlated with the intrinsic Riemann curvature of the gyri and sulci. These phreno-cortical mappings are very revealing of individual subject propensities. Coincidentally, this bre
by
RWCox
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AFNI Message Board
You seem to be trying to duplicate the pre-processing calculations of various existing DTI processing packages. The package from NIH is called TORTOISE, and has excellent eddy current corrections built-in -- among many other features. We work with the TORTOISE group, and don't really want to spend effort to replicate their years of work.
https://science.nichd.nih.gov/confluence/display/ni
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RWCox
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AFNI Message Board
I'd have to actually try this -- possibly there is some incompatibility in the software between the bilinear warp and the 3dQwarp. For me, it would be simplest if you can provide some sample data (e.g., on Dropbox or Google Drive) with copies of the commands you ran. Then I can duplicate what you did, and figure out if (a) there's a mistake in your commands, or (b) there's a mistak
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RWCox
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AFNI Message Board
QuoteWhat if there is one (or more than one) missing value (ie, subject did not respond to certain trial)? Should the 1D file be
3:1.2 10:2.1 16 21:1.1 (no reaction time--RT for time point 16)
No, this is not right. First, the program will not run if the same number of extra values are not "married" to each time value -- it will complain.
Second, I don't think there is an obv
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RWCox
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AFNI Message Board
Hola, Cesar!
No, it is not possible to directly duration modulate anything but 'dmBLOCK' (and its close relatives).
One way to do it (without changes to the 3dDeconvolve code) would be to create a 3dDeconvolve run with "-nodata NR TR", where NR is the number of time points, and TR is the time spacing of the images. For each distinct stimulus duration, create a separate s
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RWCox
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AFNI Message Board
You ask good questions. To which I don't really have answers. We've never dealt with using ANATicor on people with WM atrophy. In such a case, I would definitely not rely on the built-in AFNI 3dSeg program for finding the WM -- at least without some looking at its results to make sure they are "reasonable" -- and how one defines "reasonable" in this context I don
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RWCox
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AFNI Message Board
Does the error happen if you remove the '&' from the command line? You might be running into some timing "race condition" with multiple jobs running at one time.
by
RWCox
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AFNI Message Board
First, you are running a SERIOUSLY outdated version of AFNI. You should update and try again.
Second, you are running a lot of stimuli with no valid times, which will lead to problems in defining the regression matrix. Without seeing your data and input files, I'm not sure what could be happening. There could be a bug in the way 3dDeconvolve handles -stim_times_IM files when there is no i
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RWCox
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AFNI Message Board
Hmm. That looks like the 'find' common on your Unix isn't compatible with the 'find' common on my Mac OS X. I use 'find' to search for subdirectories that match the subject ID, and in the 'find' command, use the predicate '-depth -9' to limit the search to 9 levels of subdirectories (to avoid wandering through a vast cyberspace). Apparently,
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RWCox
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AFNI Message Board
Hmmm ... I'd like to look at this. Can you make the data files (and instructions) available to me on Dropbox or some other site?
You can send me a private message on this forum when it is ready, if you are going to do so.
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RWCox
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AFNI Message Board
From the help for afni_proc.py:
TIMING FILE NOTE: ~2~
One issue that the user must be sure of is the timing of the stimulus
files (whether -regress_stim_files or -regress_stim_times is used).
The 'tcat' step will remove the number of pre-steady-state TRs that the
user specifies (defaulting to 0). The stimulus files, provided by the
user, must match d
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RWCox
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AFNI Message Board
Encryption will slow things down somewhat, but I don't have any figures (as all NIH systems are required to use encrypted drives).
You can speed things up at the cost of using more disk space by setting various environment variables (e.g., in your .afnirc or .cshrc files)
AFNI_COMPRESSOR to NONE
AFNI_AUTOGZIP to NO
These will prevent AFNI from compressing output datasets, which will
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RWCox
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AFNI Message Board
Okay, looking at the code for 3dWarpDrive.c, I see that it is too stringent in checking for offset differences. I will fix that.
However, this message is just a WARNING, which doesn't stop the program from running. Did the results look good?
by
RWCox
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AFNI Message Board
That EPI dataset looks kind of small (in space). Only 71 mm in extent from L-R (half the brain width, roughly) and also in A-P, and only 35 mm in I-S. If you look at these two datasets in AFNI, do they properly overlap? That is, if the EPI dataset is the underlay and the brain mask dataset is the overlay, do the images overlap properly?
by
RWCox
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AFNI Message Board
Yes. To be accurate,
-gltsym 'SYM: +NF -F' \
-glt_label 1 NF_vs_F \
The label can be almost anything that's useful to help you remember. It could be 'NF-F' or 'NFminusF', if you like one of those more.
The SYMbolic expression needs to be carefully formatted. In particular, you need the space between the '+NF' and the '-F'.
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RWCox
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AFNI Message Board
The latest build of AFNI (18.0.12, Feb 2 2018) has, in addition to the BIDS-aware '-bysub' option, also has the "feature" that .jpg and .png image files will be loaded as 2D "datasets". I added this feature since some BIDS-formatted dataset collections from have .png files included that graph various things about the data. This change to AFNI allows a user to see th
by
RWCox
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AFNI Message Board
afni
-bysub This new [01 Feb 2018] option allows you to have 'sessions'
made up from files scattered across multiple directories.
The purpose of this option is to gather all the datasets
corresponding to a single subject identifier, as is done
in the BIDS file hierarchy --
** A
by
RWCox
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AFNI Message Board
Page 4 of 5
Pages: 12345