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
Page 1 of 2
Pages: 12
Results 1 - 30 of 51
Wow, yes, removing those spaces did the trick. Thanks Gang!
I can't claim to be a rookie anymore, but thanks for catching my rookie mistake.
Best,
Will
by
wgraves
-
AFNI Message Board
Dear AFNI experts,
Probably I'm just missing something obvious, this is my first time trying to run 3dICC after all, but I'm running into trouble.
Following the directions in the program help, I'm trying to run it this way:
nohup tcsh -x run_3dICC.txt |& tee diary.txt
The contents of "run_3dICC.txt" are as follows:
3dICC -prefix /home/wgraves/data/whitehall/r
by
wgraves
-
AFNI Message Board
Thanks for looking into that! I'll keep an eye out for an email and will be happy to follow up.
by
wgraves
-
AFNI Message Board
Sure thing, Paul. Thanks for getting back to me. Here's the output of "afni -ver":
Precompiled binary linux_ubuntu_16_64: Jan 24 2023 (Version AFNI_23.0.02 'Commodus')
And when I run this command:
align_epi_anat.py -verb 5 -anat MPRAGE_sag_CM+orig -epi sw3_CM+orig -anat2epi -ginormous_move -cost lpc+ -epi_base mean -child_epi sw1_CM+orig sw2_CM+orig sw4_CM+orig sw5
by
wgraves
-
AFNI Message Board
Hello AFNI experts,
Apologies if this is a repeat question. I did do a search of the message board and found no relevant results.
When using align_epi_anat.py, I tried specifying for -epi_base the option, mean. Here's my actual command:
align_epi_anat.py -anat MPRAGE_sag_CM+orig -epi sw3_CM+orig -anat2epi -giant_move -cost lpc+ -epi_base mean -child_epi sw1_CM+orig sw2_CM+orig sw4_C
by
wgraves
-
AFNI Message Board
When I run:
ps -C afni
This is what the terminal outputs:
PID TTY TIME CMD
-Will
by
wgraves
-
AFNI Message Board
Hi Rick, sorry for the delayed response. Had meetings, etc. this morning.
Here's the directory from which I'm running the demo.1.run1 script: /home/wgraves/Documents/oneSession_univar_class/AFNI_data6/realtime.demos/demo_1_run1
Also, I'm running this on a Linux machine in my lab that I'm accessing over Chrome Remote Desktop. But presumably that shouldn't matter.
I do h
by
wgraves
-
AFNI Message Board
Hmm, the only lines in my .tcshrc file that refer to /usr/local/afni/bin are these:
setenv AFNI_PLUGINPATH /usr/local/afni/bin
setenv AFNI_GLOBAL_SESSION /usr/local/afni/bin
set path = ( $path /usr/local/afni/bin )
If nothing about that strikes you as the culprit, I'll try running the script line-by-line tomorrow and let you know how it goes.
-Will
by
wgraves
-
AFNI Message Board
Dear AFNI experts,
I'm trying to run realtime demo 1 in the directory: AFNI_data6/realtime.demos. When I launch the script from the demo_1_run1 directory like this:
./demo.1.run1
I get this output:
Precompiled binary linux_ubuntu_16_64: Jan 6 2023 (Version AFNI_23.0.00 'Commodus')
Thanks go to B Feige for advice and help
Initializing: X11.. Widgets...... Input files:
by
wgraves
-
AFNI Message Board
The Language Behavior and Brain Imaging Lab (LBBIL, ) at Rutgers University – Newark, directed by Dr. William Graves, is recruiting graduate students interested in a psychology/cognitive neuroscience PhD for the Fall of 2023.
Dr. Graves and LBBIL members study the cognitive neuroscience of language and reading, with potential application to reading disorders. We also study other aspects of bra
by
wgraves
-
AFNI Message Board
Done. The output of:
afni_system_check.py -check_all
Now says: nothing to fix, yay!
So yay, thank you Rick!
by
wgraves
-
AFNI Message Board
To briefly clarify, I tried the "Quick setup" steps first, but when I run:
afni_system_check.py -check_all
this is what I get:
-------------------------------- general ---------------------------------
architecture: 64bit ELF
system: Linux
release: 5.15.0-41-generic
version: #44-Ubuntu SMP Wed Jun 22 14:20:53 UTC 2022
distributio
by
wgraves
-
AFNI Message Board
Hey AFNI folks,
I see installation instructions for Ubuntu 20, but the latest version is 22. I just bought some new Linux workstations for my lab and figured it made sense to start from a clean install of the latest version of Ubuntu. I was hoping the AFNI installation instructions for version 20 would work, but I'm running into errors. Following these instructions:
all was well until I g
by
wgraves
-
AFNI Message Board
Thank you very much for spelling that out so clearly. It worked exactly as advertised!
by
wgraves
-
AFNI Message Board
Dear AFNI/SUMA experts,
Is there any way in SUMA to display only the border outline of a region from an atlas? I'm thinking of something like the attached image from Johns et al. figure 3 (https://doi.org/10.1080/23273798.2018.1476727), but they used FreeSurfer. Apologies if I'm missing something obvious. I've searched the helps and tutorials but haven't found anything addr
by
wgraves
-
AFNI Message Board
Thanks for letting me know, Rick. I'd be happy to send you the 1D file I used for reordering if that would help you break it the way I apparently did!
Best,
Will
by
wgraves
-
AFNI Message Board
That's right, Rick. It was all processed within AFNI, using the programs you listed. I did notice what I thought was a mis-specified time field, but I wasn't sure if that was what was causing this issue with converting to NIFTI, or how to fix it. My intuition is that the 3dbucket step when I re-order the sub-briks across subjects to all be in the same order is what created the problem.
by
wgraves
-
AFNI Message Board
Thank you, Rick. This is getting more interesting. 3dcopy give the same error I got before:
3dcopy ${subj}.REML_IMs_reord+tlrc copy_reord.nii.gz
++ 3dcopy: AFNI version=AFNI_21.3.17 (Dec 30 2021) [64-bit]
** ERROR: nifti_image_write_hdr_img: NBL does not match nim
I forgot to say that in these cases a NIFTI file is actually produced. However, when I run 3dinfo on it, this is what happens:
by
wgraves
-
AFNI Message Board
Dear AFNI Experts,
I'm trying to save a HEAD/BRIK file to nii for further processing outside of AFNI. But when I run this command:
3dAFNItoNIFTI -prefix ${subj}.REML_IMs_reord.nii.gz ${subj}.REML_IMs_reord+tlrc
I get this error message:
++ 3dAFNItoNIFTI: AFNI version=AFNI_21.3.17 (Dec 30 2021) [64-bit]
** ERROR: nifti_image_write_hdr_img: NBL does not match nim
I've tried ru
by
wgraves
-
AFNI Message Board
Ha, because I didn't know the "-stim_times_IM" option in 3dDeconvolve worked that way until just now. But before I learned that from your most recent reply, I used 3dREMLfit as a drop-in replacement for 3dLSS like you suggested, and it seemed to work beautifully. So thank you Gang!
by
wgraves
-
AFNI Message Board
Hi Gang,
Thanks for the helpful reply! To be frank, I hadn't thought about 3dREMLfit. My near-term goal was to get a volume of beta-weight estimates and corresponding t-scores for each stimulus event in an event-related design (for later use with RSA). Before 3dLSS existed the only way I knew to do that was to run 3dDeconvolve once for each stimulus, modeling all other stimuli separately.
by
wgraves
-
AFNI Message Board
Dear AFNI experts,
In trying to prep data for an RSA analysis, your 3dLSS program is wonderfully efficient. However, in addition to beta-coefficient images, I'd also like to have t-statistic maps to get a metric that also includes info on variability. As far as I can tell from the help, 3dLSS does not have an option for outputting t-maps. Is there a way to have it do this that I'm ju
by
wgraves
-
AFNI Message Board
Hello AFNI developers,
Sorry for throwing a problem out there right before Memorial Day weekend, but I figured it was worth mentioning.
When I run auto_warp.py it fails to find "./base.nii".
Here's the actual command, in case that helps:
auto_warp.py -base /usr/lib/afni/bin/MNI152_2009_template_SSW.nii.gz -input /usr/lib/afni/bin/TT_N27+tlrc -output_dir /home/wgraves/data/ABIDE
by
wgraves
-
AFNI Message Board
Just tested it with your latest version and it works like a charm now. Thank you!
by
wgraves
-
AFNI Message Board
Dear AFNI experts and developers,
Hopefully I'm just missing something basic, but this one has me stumped.
I'm trying to use afni_proc.py to pre-process some resting state fMRI data. For a couple of the subjects, alignment of the structural to the functional was giving me trouble until I used the "-edge" option. That fixed the alignment in separate testing using align_epi_an
by
wgraves
-
AFNI Message Board
Hi Paul,
Thank you for the prompt and helpful reply. Here's the output of afni -ver:
Precompiled binary linux_ubuntu_16_64: Mar 3 2021 (Version AFNI_21.0.13 'Titus')
When I open the QC webpage output for this analysis, I do not seem to have the ve2a and va2t QC blocks. (See attached screen shot.)
I did visually check, and indeed @SSwarper appeared to do a good job aligning t
by
wgraves
-
AFNI Message Board
Hello AFNI experts,
As much as I dread asking for help in public, this issue has me stumped. I'm trying to follow afni_proc.py example 11 to pre-process some resting state data. Following that example, I first ran @SSwarper to calculate the transform of the anatomy to MNI space. Then I provided those images to afni_proc.py, along with -align_opts_aea that I separately verified to properly a
by
wgraves
-
AFNI Message Board
The Psychology Department at Rutgers University in Newark, New Jersey, is recruiting a full-time research assistant to work in Dr. Miriam Rosenberg-Lee’s Mathematics, Reasoning and Learning Lab and in Dr. William Graves’ Language, Behavior and Brain Imaging Lab. The Mathematics, Reasoning and Learning Lab studies the cognitive neuroscience of mathematics learning, with applications to typical and
by
wgraves
-
AFNI Message Board
The Math & Computer Science Department at Rutgers University -- Newark is hiring an Assistant Professor (or early Associate Professor) position. Details on the position and how to apply are here:
by
wgraves
-
AFNI Message Board
Page 1 of 2
Pages: 12