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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 1291 - 1320 of 2305
Oh, it looks like this issue of getting R's brms on CentOS has already been solved by an AFNI user, and the solution is posted here:
(you might want to look at the earlier parts of the thread, too).
--pt
by
ptaylor
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AFNI Message Board
Howdy-
I will assume that running "rPkgsInstall -pkgs ALL" as described here:
doesn't work to update things.
It might be that if you have updated your R version, then you need to update the existing packages before installing more. So, to try this, start by typing this in a terminal to enter the R environment:
R
And then copy+paste of each of these there individuall
by
ptaylor
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AFNI Message Board
Hi-
What OS is your computer? and what version of R do you have?
Having the output of this copy+pasted:
afni_system_check.py -check_all
would be useful.
--pt
by
ptaylor
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AFNI Message Board
Yeah, there is a new problem on Macs with the threshold bar.
Bob put in a fix into the *latest* build of AFNI (June 3, I believe)-- so you can get that one. The jittering will be gone.
What *will* happen sometimes is that the threshold bar will shrink to about 50% size or so; the "Thr" at the top of the threshold bar has now been turned into a button-- left clicking on it will p
by
ptaylor
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AFNI Message Board
Hello-
The next AFNI Bootcamp at NIH will have its main session running Nov. 4-8, and there is an optional/alternative DTIsession on Nov. 8 (*note that it is Friday this time*).
There is no registration fee for the Bootcamp, but attendees must pay all their own expenses (e.g., lodging, travel, food, fancy coffees).
The registration page is here:
along with preliminary schedules and
by
ptaylor
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AFNI Message Board
Hi, Lz-
Indeed, I haven't been able to get to this yet. In large part, because it would involve several other softwares that I am not familiar with. So, if you have done the hard work and know the changes that should be made, then that should speed things up.
Are you saying that the only change needed is that the voxel_order header field needs to use the opposite of AFNI's voxel
by
ptaylor
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AFNI Message Board
The following paper by Bob has been accepted in Brain Connectivity, and a public draft version is available here on bioRxiv:
Read it, enjoy it, live it.
by
ptaylor
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AFNI Message Board
Hi, Michael-
AFNI/SUMA creates standardized meshes. So, by default you can display your results (niml.dsets?) on any mesh. Therefore, you can load up one of the pre-made MNI meshes (e.g., available here: ) as the "underlying" mesh, and display your results there.
--pt
by
ptaylor
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AFNI Message Board
What is the output of:
A)
3dinfo -ad3 -o3 -orient -prefix 1_MPRAGE+orig $File_Path/MNI152_2009_template_SSW.nii.gz
and B)
3dCM 1_MPRAGE+orig $File_Path/MNI152_2009_template_SSW.nii.gz
?
--pt
by
ptaylor
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AFNI Message Board
Hi, Tianshu-
3dNetCorr is a program for calculating correlation between the average time series of any number of ROIs.
Is that what you want?
--pt
by
ptaylor
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AFNI Message Board
Hi, Zhihao-
I don't think @RetinoProc can be retrofitted with that capability too easily without re-writing the whole thing.
Note that it does have an "echo_edu" option, so that each AFNI program will display on the command line its exact set of options; that could be combined with piping+teeing to an output text file, to see what each command is doing exactly. There is als
by
ptaylor
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AFNI Message Board
Hi, Francesco-
Hmm, having an empty file there (so, a file is created, but it is 0 bytes?) is odd.
Do you have an output.* file, that "tee"s the processing stream when you run it? That is, either using the "-execute" option, where one is made automatically, as described here:
-execute : execute the created processing script
If this optio
by
ptaylor
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AFNI Message Board
Hi, Steph-
OK, that sounds like you are doing the correct things, and the output does sound a bit odd.
What does this mean: "Freesurfer annotation file with 300 parcels"? The map of target ROIs among which one wants to search for pairwise connections should be a file of integer values, and each ROI is defined as the set of voxels with a given integer. String labels can be attach
by
ptaylor
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AFNI Message Board
Hm, are you sure that the "spec" file exists with that name/in that location? There is this error message that makes it seem like it doesn't:
...Error SUMA_Read_SpecFile: File indt_std.141.SUBJ_001_both.spec does not exist or cannot be read.
It looks like you need to change the "SUBJ_001", which is the subject ID in the example, to your own?
--pt
by
ptaylor
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AFNI Message Board
Hi-
Unfortunately, there isn't. @chauffeur_afni (and @snapshot_volreg, and some other AFNI-driving programs) open AFNI in a virtual environment using xvfb, so that AFNI doesn't have to be opened in a graphical interface; that means they can be run remotely and headlessly. The same is not possible with SUMA, alas.
We have bits&bobs of QC imaging things in SUMA, but there i
by
ptaylor
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AFNI Message Board
Hm, I wonder if some variable got set incorrectly in a ~/.*rc during the setup.
Can you please run the following:
afni_system_check.py -dot_file_pack DOT_FILES.tgz
and then send the created DOT_FILES.tgz file to me? (I will PM you instructions for that.)
--pt
by
ptaylor
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AFNI Message Board
Hi-
I think we'll need some more specifics to know what might be happening. What system are you on (linux, mac, windows-linux)?
What does this mean: "whenever I put any directory change in"? Can you please copy+paste an example of:
+ a command you are using,
+ the output given
+ and the directory run from (output of typing "pwd" in a terminal)
What is the ou
by
ptaylor
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AFNI Message Board
Hi, JW-
OK, that's as I suspected-- you have a version of AFNI binaries that aren't updated anymore, and that have other dependencies. Please run the following to update your AFNI binaries to the more modern 10.12_local version (and this will also update your AFNI version to something much more recent):
@update.afni.binaries -defaults -package macos_10.12_local
I think that sho
by
ptaylor
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AFNI Message Board
Hi, Walker-
Thanks for looking at this so closely.
One difference is that the anatQQ volume has gone through some preliminary "polishing" as part of the @SSwarper processing. By default, the input anatomical is put through 3dUnifize and 3danisosmooth. So, there is some adjustment of brightness and blurring due to the combination of those.
If you don't want one or the oth
by
ptaylor
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AFNI Message Board
Hi, JW-
What is the output of the following:
afni_system_check -check_all
? (Please copy+paste.)
--pt
by
ptaylor
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AFNI Message Board
Ah, this 3dNwarpXYZ usage seems a much easier solution than the one I suggested.
--pt
by
ptaylor
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AFNI Message Board
Hi, Brady-
My guess is that some are being squashed into oblivion by the regridding in some cases. That is, by applying the NN interpolation when applying the warp, you are preserving the integer values in your data set. However, it looks like your Undump "ROIs" are just individual voxels: in the case that the warping process leads to a contraction of the source grid, your individ
by
ptaylor
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AFNI Message Board
Hi, Larry-
I am afraid I don't see how that could be accomplished. Perhaps something involving huge amounts of Monte Carlo simulations/bootstrapping, but it seems hard to get an objective answer to that question that wouldn't be highly assumption- or model-dependent, as well as one that would generalize.
Is there a way that you can reformulate that question of interest into somet
by
ptaylor
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AFNI Message Board
Hi-
Those aren't really errors, just suggestions.
The second one is probably the more useful one to do something about; the first is just a style choice (many AFNI scripts are written in tcsh, so if you use a bash terminal, you might have to alter some things like variable definition syntax-- but that is really not a major thing).
To deal with the second one, you can copy+paste t
by
ptaylor
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AFNI Message Board
Hi, Priya-
There are some educational resources you can browse about AFNI in general and afni_proc.py specifically, located here:
There are some particular AFNI Bootcamp recordings here:
and here:
for example.
--pt
by
ptaylor
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AFNI Message Board
Hi-
There is some description of this process in this help file:
See "Adding a new colormap into AFNI".
What does your colorbar look like, might I ask?
--pt
by
ptaylor
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AFNI Message Board
Hi-
3dMVM and 3dLME seem to be compatible with a number of R versions. I woudl expect R v3.3 or 3.4 would be fine for those.
Other/newer programs (such as MBA and RBA) might require newer R version. *However*, we have had trouble with installation for those, so at the moment I wouldn't upgrade just to upgrade (we have to contact the authors of a particular package for assistance in th
by
ptaylor
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AFNI Message Board
Hi, Steph-
There are several things to look at, such as where FA>0.2 (-> should match WM in ~healthy human adults). You can also look at DEC maps. Some description in the FATCAT_DEMO2 are provided here:
--pt
by
ptaylor
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AFNI Message Board