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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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Results 31 - 51 of 51
Since Bob helped me with this by individual email, I thought I'd quickly post the solution, in the unlikely event anyone else runs into the same problem.
The error came from my having only one stimulus event in my regression matrix file. The old way of getting individual stimulus estimates, using only 3dDeconvolve, required modeling one stimulus event at a time, so I was just assuming the s
by
wgraves
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AFNI Message Board
Just to briefly follow up with this, it still has me stumped. I double checked, and all the columns are indeed the same length (corresponding to 625 total TRs). I would be happy to upload the regression matrix from 3dDconvolve if that would help. In running 3dDeconvolve, I only have one -stim_times_IM regressor, and all the stim_times regressors use the "BLOCK(0.5,1)" style HRF. So 3dDe
by
wgraves
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AFNI Message Board
Dear AFNI Experts,
In trying to get trial-specific beta-weight estimates to eventually use with MVPA analyses, I'm using 3dDeconvolve with its "-x1D" option to save out a regression matrix, which I then input to 3dLSS. My individual stimulus regressor ends up being in column 7, and when I run 3dLSS on a single stimulus (having modeled all other stimuli separately in 3dDeconvolve
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wgraves
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AFNI Message Board
This looks great! One question: Originally the link you gave to the AFNI Bootcamp website worked, but now it just re-directs to the website usage summary page. If that could be fixed, it would really help.
Thanks,
Will
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wgraves
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AFNI Message Board
A research assistant/lab manager position is available in the Language Behavior and Brain Imaging Lab (http://lbbil.rutgers.edu/) at Rutgers University in Newark, New Jersey. We primarily study the cognitive neuroscience of reading, with potential application to reading disorders. We also study other aspects of brain and language, including concept retrieval and speech production. Research is per
by
wgraves
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AFNI Message Board
Hi Rick,
Thanks for the prompt reply. Yes, if I trim the "reorder.1D" file to be only, say, 10 lines (instead of the original 287), then the command does work. But is doing this for 287 sub-briks really running up against a hard-coded limit? And if so, I'd love to know a way to get around this. I'm trying to re-order sub-briks of each subject to match an example subject, an
by
wgraves
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AFNI Message Board
Also, I get the exact same behavior (works with -dry, crashes when run for real) when using 3dTcat in the way I described for 3dbucket.
by
wgraves
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AFNI Message Board
Dear AFNI Experts,
When trying to re-order briks in a existing bucket image, I'm using this command:
3dbucket -fbuc -prefix ${subj}_LS-S_reord ${subj}_LS-S+orig'[1dcat reorder.1D]'
Where "reorder.1D" is a simple text file with 287 entries in a single column. Here's the error message I'm getting:
++ 3dbucket: AFNI version=AFNI_2011_12_21_1014 (Dec 8
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wgraves
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AFNI Message Board
That sounds great, Gang. Thanks for letting me know you're on the case!
-Will
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wgraves
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AFNI Message Board
Hi James,
Thanks for the quick reply! I did see that thread from a few months ago, but I didn't realize the readline() vs. scan() issue specifically impacted the ability to feed a text file of arguments to Gang's existing interactive script.
Gang, any chance this is on the docket to be fixed for the next update? For me it basically determines whether or not I can use 1dSVAR.
Th
by
wgraves
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AFNI Message Board
Dear AFNI experts (especially Gang),
In trying to run 1dSVAR.R, I can get pretty far using the interactive interface, but I've been trying to make the process workable by creating a script I can give to 1dSVAR that contains all the answers to the interactive questions. Unfortunately, when I run my little custom script:
~/data/ambig_sam/fmr_scripts/make1dSVAR.csh
It errors out early on
by
wgraves
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AFNI Message Board
A research assistant/lab manager position is available in the Language Behavior and Brain Imaging Lab (http://lbbil.rutgers.edu/) at Rutgers University in Newark, New Jersey. Much of our research is devoted to the cognitive neuroscience of reading, with potential application to reading disorders. Other aspects of brain and language studied in the lab include concept formation and speech productio
by
wgraves
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AFNI Message Board
The Department of Psychology at Rutgers University-Newark anticipates hiring at the assistant professor (tenure track) level. We seek applications from individuals with specializations in areas of Psychology and Neuroscience that primarily use fMRI as a methodology. Examples of research areas of special interest include social, developmental and cognitive neuroscience.
Applicants that incorpor
by
wgraves
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AFNI Message Board
Dear Gang or other experts,
I'm trying to do a quick demo of 1dSVAR.R for a class I'm teaching, and I'm running into an error at the individual subject level. It seems to work fine through the point of specifying all the input files and the lag order, but when it tries to do a quality check, I get this:
Error in B <- coef(x$varresult[]) :
number of items to replace is
by
wgraves
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AFNI Message Board
Hi Rick,
Thanks for the quick response. You don't have a system to test it on? I thought you folks at AFNI Central were a bunch of Mac enthusiasts. No?
Anyway, it displays the same behavior without X11 running. In fact, when I try to launch X11, the same popup window I described earlier comes up, saying X11 needs to be installed, but pressing the button just takes me to a message about
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wgraves
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AFNI Message Board
Dear Team AFNI:
Against my better judgment, I upgraded my Mac OS to Mavericks (10.9.3). Now AFNI won't open, even after I ran "@update.afni.binaries". First I tried specifying -package as macosx_10.9_Intel_64, but the script gave an error message that looked like it was having a problem un-tarring it. Same thing for 10.8. When I tried 10.7, it gave no errors and looked like it s
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wgraves
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AFNI Message Board
The Rutgers University Department of Psychology in Newark, New Jersey, has an opening for a computer System Administrator. The position involves providing general IT support for the department, including several functional neuroimaging labs. To see the official description and apply, follow this link:
Rutgers is the state university of New Jersey, and its Newark campus is in the state’s larg
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wgraves
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AFNI Message Board
Hi Ziad,
It seemed like the problem came up when the @auto_tlrc script called 3dZeropad. I thought I remembered seeing on the message board somewhere that someone ran into a problem with that program and the solution was to update AFNI. So I tried that, and it worked!
Thanks,
Will
by
wgraves
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AFNI Message Board
Dear Team AFNI,
When trying to run this command:
@auto_tlrc -no_ss -base /usr/share/afni/TT_N27+tlrc -input maxAnat_al+orig
I get the following message and no useable output image:
Padding ...
++ 3dZeropad: AFNI version=AFNI_2011_12_21_1014 (May 3 2012) [64-bit]
++ output dataset: ./__ats_tmp__ref_TT_N27_40pad+tlrc.BRIK
Resampling ...
invalid master dataset <__ats_tmp__ref_TT_
by
wgraves
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AFNI Message Board
A research assistant/lab manager position is available in the newly formed Language Behavior and Brain Imaging Lab at Rutgers University in Newark, New Jersey. Much of the research in the lab is devoted to the cognitive neuroscience of reading, with potential application to reading disorders. Other aspects of brain and language studied in the lab include concept formation and speech production. R
by
wgraves
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AFNI Message Board
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