Show all posts by user
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
This is a combination of cheap tricks that might work for you:
(1) right click on the intensity scale to the right of the image image, and you get a popup menu -- on that menu is a toggle on/off button "Automask?" -- click that button to the on state
(2) At this point, the "Choose Zero color" option on that same popup menu might work for you.
Or if that still leaves u
by
Emperor Zhark
-
AFNI Message Board
Thanks for this message. I have only tried Xvfb a few times to make sure it works, and not recently.
If there were a way to detect this situation, the "detach" function could be automatically skipped.
I suppose it might be done with the xdpyinfo command or something like it.
by
Emperor Zhark
-
AFNI Message Board
If the FMRI signal changes were large (say 10% or more), then using a non-task (pre-stimulus) baseline would make some sense. For example, suppose that the task-state is about 1/2 the duration of the experiment. Then if the baseline is 'b' and the signal change is 'x', then the mean signal would be about 'b+x/2', so using this mean would give a fractional ("pe
by
Emperor Zhark
-
AFNI Message Board
No, but that's not a bad idea. But do you have such a dictionary? And is it re-distributable?
by
Emperor Zhark
-
AFNI Message Board
Sorry, this is a coordination problem we're working on, and it should be fixed "real soon now".
by
Emperor Zhark
-
AFNI Message Board
Cesar is right, that the "tim" functionality is inside the AFNI GUI now.
The program you are thinking of was FD2, which read in a sequence of 2D images and did the functional correlation mapping. It was basically a merger of the fim program (for correlations) and the FD program (for display of 2D time series).
When I started AFNI in 1994, it was at first to be a 3D version of FD2
by
Emperor Zhark
-
AFNI Message Board
You are correct that the saved dataset is not the same as what you were seeing. The saved dataset is the actual correlation map. The visualization is "on the fly" editing, for thresholds, colorization, and clustering, all applied interactively -- but not affecting the correlation 3D volume, which is what "Save" works with.
by
Emperor Zhark
-
AFNI Message Board
"Killed" is a one word message from Unix that the operating system killed your program -- almost always this happens because the program used up too much memory.
You can add the "-usetemp" option to 3dcalc, which will make it run slower but might let it process a very big input file. If you are lucky, that is.
by
Emperor Zhark
-
AFNI Message Board
From this day forward, we will no longer be building AFNI for Solaris 2.9 (or any version). The last users at NIH have evaporated and migrated.
Historically, AFNI was first written on HP-UX, and thence moved to SGI IRIX and Sun Solaris -- all in 1994. All 3 are now consigned to the footnotes of AFNI's biography.
by
Emperor Zhark
-
AFNI Message Board
3dTsmooth was modified today to include the adaptive mean filter. It will be rebuilt on Monday night and be available Tuesday morning (06 Oct 2014 -- anniversary of the attack on Frodo at Weathertop).
by
Emperor Zhark
-
AFNI Message Board
Github is in our mind's eye as well -- but getting it done is a matter of finding time.
by
Emperor Zhark
-
AFNI Message Board
Are there ANY similarities between the two results?
I would expect the default level of refinement in 3dQwarp to produce decent results in the center of the brain, but not so much in the periphery of the cortex. Running the program with the options
-pblur -minpatch 9
(that is, to the finest level of matching) might work better. Of course, it will be slower.
by
Emperor Zhark
-
AFNI Message Board
The warping looks right to me. Of course, the warps are computed from just the #0 sub-brick of the input datasets to 3dQwarp, and then are applied to all sub-bricks in the 3dNwarpApply commands -- I suppose that is clear from the documentation.
by
Emperor Zhark
-
AFNI Message Board
There is no easy way to implement the adaptive mean function used in the interactive AFNI using 3dTsmooth or 3dcalc. By far the simplest approach would be to put it into 3dTsmooth itself.
But why do you want it?
by
Emperor Zhark
-
AFNI Message Board
I suppose we could ignore the SIGPIPE signal, but the default is to terminate the process. So I put it in the list of traceback-ed signals. A few programs that explicitly open and write to pipes do set SIGPIPE to be ignored.
by
Emperor Zhark
-
AFNI Message Board
In my posting, I somehow assumed that you were asking a question about 3dttest++, not 3dGroupInCorr. That's a somewhat different problem, and also requires thinking. In this case, my first reaction is that the program would have to be modified to do the test. And that in turn would require choosing which kind of test on the covariate slopes would be desired.
by
Emperor Zhark
-
AFNI Message Board
As far as I can tell, it is possible to carry out the paired test with differing covariates between the 2 samples only by manually subtracting the data pairs and then doing a 1 sample test with 2 covariates. That is:
Definitions:
xi = first sample voxel value, ith subject
yi = second sample voxel value, ith subject
ci = first sample covariate value, ith subject
di = second sample covari
by
Emperor Zhark
-
AFNI Message Board
The old 3dttest program is still in the distribution precisely because it has these rarely used options that I did not want to put into 3dttest++, which is a more complex program since it has to deal with covariates.
by
Emperor Zhark
-
AFNI Message Board
That's a very interesting question -- which is a way of saying I'm not sure. When doing a paired test where the same covariate has different values in each half of the pairs, it's a little confusing to me as to what the statistical mode/question should be. I'll have to think about it some.
by
Emperor Zhark
-
AFNI Message Board
You could do this with the InstaCorr plugin, by specifying the "Start,End" parameters.
by
Emperor Zhark
-
AFNI Message Board
This bootcamp is now fully registered, and new enrollees are being put on a waitlist. So if you registered and then will NOT be coming, please email Brian Pittman to un-register -- so that someone else can come in your place.
by
Emperor Zhark
-
AFNI Message Board
The code miraculously heals itself -- sort of like the immune system maybe.
by
Emperor Zhark
-
AFNI Message Board
This doesn't happen on my Macintosh, nor on a Linux machine. The line numbers you have don't correspond to current code, so it's hard to see where these errors are being detected. Can you update your version of AFNI to the current version and try again? If you compile from source code, the code has just been updated in the last hour. If you need a pre-compiled binary version, t
by
Emperor Zhark
-
AFNI Message Board
The program doesn't "know" that you just masked the data with your 3dcalc expression. The author (me) assumed the worst, that you changed the values in some arbitrary way, so that they are no longer from well-known statistical distributions -- for example, if you took the cube root of a t-statistic, it would no longer be useful.
You can re-attach the codes that mark various sub
by
Emperor Zhark
-
AFNI Message Board
If you do not have the event onset (or duration?) times, then you are missing a serious part of the experimental data!!
There are ways to guess the times, but those are not likely to be successful unless you have a block design (long duration events) activation cycles visible in major areas such as visual and/or motor cortex.
You could do an ICA type of analysis, which is very different tha
by
Emperor Zhark
-
AFNI Message Board
Very short notice, but here's an FMRI-oriented job opportunity in the extramural side of the NIH:
by
Emperor Zhark
-
AFNI Message Board
Not exactly a mention, but an allusion: in Nancy Andreasen's article on creativity, the FMRI figure (about halfway down) is clearly taken straight from AFNI.
http://www.theatlantic.com/features/archive/2014/06/secrets-of-the-creative-brain/372299/
Our 15 milliseconds of fame is here!
by
Emperor Zhark
-
AFNI Message Board
No. I just compiled and made available the new binaries macosx_10.8_icc.tgz which are what you should download and install. These should work better for you, I hope.
There was a delay, since I had to fix a bug in the new -pblur option in 3dQwarp, that was kind of subtle, and I didn't understand it until sometime Saturday.
by
Emperor Zhark
-
AFNI Message Board