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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
Results 2281 - 2305 of 2305
Hi, Rick-
Wow, thanks for the speedy reply-and-fix. I will give your first suggestion of editing a try, and will eagerly await the update in the full version-- now I can take that off my list for Santa.
Thanks,
pt
by
ptaylor
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AFNI Message Board
Hi--
Can I use uber_subject but do all the processing and leave the output in the native/functional space instead of a tlrc/mni-type space?
Thanks,
pt
by
ptaylor
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AFNI Message Board
Is it too inelegant to calculate the mean before filtering:
3dTstat -mean -prefix MEAN_FILE FILE
then to regress out/filter what you want, getting FILT_FILE,
and to add back the original mean:
3dcalc -a MEAN_FILE -b FILT_FILE -expr 'a+b' -prefix FINAL_FILE
?
--pt
by
ptaylor
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AFNI Message Board
So, did you install the GSL libraries to sort out that issue? Or did changing the glib name chase away two errors with one stone?
Probably somebody else should weigh in on this, but I think that I would probably use fink or something to get the real glib libraries that go with the appropriate version... I believe that the Glib libraries are used for compiling/running C.
Would doing:
su
by
ptaylor
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AFNI Message Board
I think someone else on the MB had that latter error as well, and the solution was to download the GSL (the GNU Science Library), which can be gotten via fink: `sudo fink install gsl'. Otherwise, they are available via the GNU website: www.gnu.org .
--pt
by
ptaylor
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AFNI Message Board
Hi,
Were these commands working on a lower-number version of your Mac OS? Or is this the first time you are running them on the Mac? In the latter case, I wonder if you don't have GSL (the GNU Science Library) downloaded, which can be gotten via fink:
`sudo fink install gsl'. Otherwise, they are available via the GNU website: .
Please let me know if that solves the issue
by
ptaylor
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AFNI Message Board
At user request, a simple program to supplement 3dTrackID has been added to AFNI, in order to be able to map the tracks (*.trk file) from one space to another. The name of the program is "map_TrackID."
One can use AFNI's 3dAllineate program to calculate a map from, say, native subject space A to standard space B and save the associated transformation matrix with "-1Dmatrix
by
ptaylor
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AFNI Message Board
Hi-
Have found (and hopefully solved!) the problem-- the AFNI error message complaints were correct that I had made a mistake during the freeing of the matrices in 3dReHo. I believe that this has been fixed now, and the improved 3dReHo is now included in AFNI if you update your version. Thanks for pointing this out, and please let me know that the new version works smoothly for you.
Cheer
by
ptaylor
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AFNI Message Board
I believe that this message (and the similar complaint in the preceding Message Board entry) is given whilst freeing variables after having run successfully and after the outputs have been created. However, I'm sure it's annoying to see. Can I ask what system your data is being run on, and how your data set was created?
Thanks,
pt
by
ptaylor
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AFNI Message Board
Hmm, what is the specific commandline you are using?
Thanks,
pt
by
ptaylor
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AFNI Message Board
Hi, Rick-
Well, since I'm located just outside of Cape Town these days, my postings were actually part of a normal day-- I unfortunately can't take credit for working diligently into the wee hours of the morning.
And now, in the clear light of the afternoon here, I see now what was meant by `upper left of the GUI'.... He meant the `upper left of the GUI'. And that (usin
by
ptaylor
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AFNI Message Board
Hmm, well, I've changed: AFNI_SLAVE_FUNCTIME, AFNI_SLAVE_THRTIME and AFNI_SLAVE_BUCKETS_TOO all to YES in the ~/.afnirc file (and I had to add a line for the third one to be included; I've also tried using those in the commandline with -D, as well), but nothing appears to change when that happens-- when I plot an overlay, the default OLay is #0 and Thr is #1, and even if I change the OL
by
ptaylor
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AFNI Message Board
Hi-
I have a 4D data set I'd like to flip through, say of Z-score values. I'd like to set a threshold of Z=2.3 and then flip through to see what stick arounds per sub-brick. However, I admit that I am lazy enough to be annoyed to have to click *two* GUI buttons per iteration, having to change both the OLay and Thr to be the same sub-brick index each time... Is there a way that I ca
by
ptaylor
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AFNI Message Board
Hi-
I am not aware of any available software packages for the fast
marching tractography (FMT). I'm pretty sure that there is none in
AFNI, though I will point out that there is both a deterministic and a
probabilistic tractography program in AFNI. Particularly the latter
was written (disclosure: by me) with the aim of coupling DTI and fMRI
studies. It's based on an improveme
by
ptaylor
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AFNI Message Board
Yes, I think any version after Aug 24. should have them-- I updated my binaries then to check that the programs were available, and my version is:
[]
--pt
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ptaylor
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AFNI Message Board
Hi--
The paper for the tractography algorithm used in 3dTrackID and 3dProbTrackID is now finally published:
Taylor PA, Cho K-H, Lin C-P, Biswal BB (2012) Improving DTI Tractography by including Diagonal Tract Propagation. PLoS ONE 7(9): e43415. doi:10.1371/journal.pone.0043415
(should be available at: ).
It describes the motivations and method of FACTID and also comparisons with a number
by
ptaylor
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AFNI Message Board
Hi-
Firstly, I'm sorry for the late reply.
Secondly, I think the problem is trying to underlay an anatomical (presumably, T1?) image beneath the tracks. That will surely be a much higher resolution than the individual DWIs (and hence, DTIs and related data sets), I would think. The tractography is images can be overlaid on, for example the FA or MD images quite easily, as those all h
by
ptaylor
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AFNI Message Board
There are now two new programs as part of AFNI for calculating
widely-used resting state functional connectivity (RSFC) parameters
for resting state fMRI (rs-fMRI). These are: A) 3dRSFC and B) 3dReHo.
Both programs should be:
+ simple to use,
+ fairly efficient time/memory-wise,
+ provide informative parameters for RSFC studies in a single (or
nearly so) swoop.
The programs
by
ptaylor
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AFNI Message Board
Oh. Ok, well, actually the same thing applies.
+ If you have multiple DW factors (for example, using b=500 for some and b=1000 for others), then you have to use the `-bmatr' form/options.
+ If you have just a single b=0 image and a single, DW factor, you can use the `-grad' option/form.
+ If you have multiple b=0 images, you will also have to use the `-bmatr' form, and each
by
ptaylor
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AFNI Message Board
Hi-
(Apologies in advance for bright coloration of formulae below, but I couldn't get the useful spacing to be enforced without it...)
I should first note, that 3dProbTrackID currently doesn't use the b-value for anything, actually (future versions might, so it's there now, but no need to worry about having multiple values). You can just put `1000' or anything really as
by
ptaylor
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AFNI Message Board
Also, what is the output when you type `AFNI -version'?
Thanks,
pt
by
ptaylor
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AFNI Message Board
A note for TORTOISE users interested in using this tractography:
TORTOISE outputs via DIFF_CALC have slightly different naming and file conventions than `3dDWItoDT -sep_dsets'. The various inputs to new AFNI tractography programs (3dTrackID, 3dDWUncert, 3dProbTrackID) are mostly assumed to have come from 3dDWItoDT... But never fear! I believe that there will soon be an option in the DI
by
ptaylor
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AFNI Message Board
Hi,
Yes, that's right, the `-sep_dsets' has to be used. My thought was it would be the easiest way to allow non-3dDWItoDT users to use the tractography programs as well, as well.
And yes, 3dDWUncert does require GSL.
Thanks for pointing out about the 3dProbTrackID; I'll check with Ziad about that.
--pt
by
ptaylor
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AFNI Message Board
A set of diffusion tensor (DT)-based deterministic and probabilistic
tractography programs are now available for use in AFNI. These include:
deterministic tractography (3dTrackID), probabilistic tractography (3dProbTrackID), and a program to estimate DT parameter uncertainty, for use with probabilistic tractography (3dDWUncert).
These have been variously developed, code/implemented and test
by
ptaylor
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AFNI Message Board