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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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The Laboratory for Rehabilitation Neuroscience (lrnlab.org), located in the Department of Applied Physiology and Kinesiology, College of Health and Human Performance, at the University of Florida seeks a candidate for a NIH funded postdoctoral position focused on neuroimaging of movement disorders.
QUALIFICATIONS: The candidate should have a Ph.D. in psychology, neuroscience, engineering, phys
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archerdb
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AFNI Message Board
Hi Daniel,
The output of whereami -show_atlases shows all of the atlases with a description next to it. The description for each atlas is as follows:
/home/user/abin//atlas
Could the error be a result of the two "//" before the atlas? So it's looking for a path that doesn't exist? How would I edit this?
Thanks,
Derek
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archerdb
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AFNI Message Board
Hi Rick,
I unset the LD_LIBRARY_PATH and tried to access "Where Am I?" from the GUI. AFNI still shut down when I tried this.
Thanks,
Derek
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archerdb
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AFNI Message Board
Hello --
The output of the suggested command is below:
-------------------------------- general ---------------------------------
architecture: 64bit ELF
system: Linux
release: 4.4.0-53-generic
version: #74-Ubuntu SMP Fri Dec 2 15:59:10 UTC 2016
distribution: Ubuntu 16.04 xenial
number of CPUs: 32
apparent login shell:
by
archerdb
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AFNI Message Board
Hello!
I am attempting to right click in the AFNI window and choose "- Where Am I?". When I choose this, I don't get an error in the command window but the AFNI windows all close.
If I try to run the whereami command in the command window, however, I get output. Any idea why it would be doing this?
Thanks!
Derek Archer
by
archerdb
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AFNI Message Board
Hi pt --
Adding the Tsmooth to IsoSurface made it look much better, thanks!
One final question -- I usually use the bw20 cmap file for my brains, and am having trouble getting that to show up on the dialog box. Where would this file be located? I'm interested in saving it to my working directory so I can select bw20 by using the "New" button.
Thanks,
Derek
by
archerdb
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AFNI Message Board
Hi pt --
These are volumes that were created with IsoSurface. I then load these volumes in with the following command in a script:
Group = TT_N27_plus
StateDef = smoothwm_plus
NewSurface
SurfaceFormat = ASCII
SurfaceType = GIFTI
SurfaceName = lh.smoothwm.gii
LocalDomainParent = SAME
SurfaceState = smoothwm_plus
EmbedDime
by
archerdb
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AFNI Message Board
Hello!
I have been using SUMA to show 3d images of white matter tracts. This summer, I was able to open the tracts and they looked very smooth; however, when I try to open the same files now they look blocky. Is there something that I can change to get smooth tracts again?
I've attached both images at the below link so that you can see the difference.
SUMA_Issue
Thanks,
Derek
by
archerdb
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AFNI Message Board
Hi Bob --
I have completed cluster thresholding, and do not get any significant task based activity for any of my tasks, which is why I thought I was getting the FDR q warning. I am thinking there is something wrong with my data analysis and that is why I'm not getting any significant activity anywhere. So far, I have checked the stim time files and head motion, and there doesn't
by
archerdb
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AFNI Message Board
Hi Gang and Bob --
I should have phrased my question a little better.
I am getting the FDR q warning with my data when running 3dttest++, and I haven't received this warning before. Because of this, I am assuming there is an error somewhere in my pipeline. I have checked my stim times, and removed subjects who I believe inaccurately performed the task of interest. I've also
by
archerdb
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AFNI Message Board
Hello everyone!
I keep getting the bellow error when running 3dttest++:
Warning: Smallest FDR q [1 task_Tstat] = 0.5656 ==> few true single voxel detections
Is there a specific reason I would be getting this error?
Thanks,
Derek
by
archerdb
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AFNI Message Board
Hello,
I like to use the red, blue, and green monochrome colors in SUMA; however, I would like to create additional colors. Would I use MakeColorMap to do this?
Is it possible to just make a local copy of the red monochrome file, for instance, and edit it to make a new color?
Thanks!
Derek
by
archerdb
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AFNI Message Board
Hello Y'all,
I'm doing a pain experiment in the scanner in block design. The subject first rates his resting pain, then experiences an external pain eliciting stimulus, then rates that pain on a 0 to 10 scale, then he rests, and then rates this resting pain and so on. So, the design looks like this:
rest rate1 pain rate2
rest rate1 pain rate2 ...
The problem is that a small res
by
archerdb
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AFNI Message Board
Hello everyone,
I have a couple of questions about the best way to design my experiment.
I have two tasks and am doing block design. I am interested in each task separately and also their contrast. Both tasks will activate the same parts of the brain, but to different levels. .
I could put each task in a separate scan or I could intermix them so that I have both tasks in both scans and
by
archerdb
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AFNI Message Board
Hi Gang!
Ok, so I do have 6 values per subject. I've set up my analysis using 3dMEMA, and is setup as below:
3dMEMA -prefix low_file \
-set low \
sub_00 'beta' 't_stat' \
sub_01 'beta' 't_stat' \
...
...
sub_15 'beta' 't_stat' \
-HKtest \
-covariates Covariates.txt \
-mask Group_mask
The Covariates.txt fi
by
archerdb
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AFNI Message Board
Hi Gang,
To use 3dcalc to get the contrast, do I just subtract the beta coefficients? How would I get t-values for that?
I have 6 independent variables, and they are all fractional anisotropy values of different white matter tracts. So I have a value for each person.
Thanks!
Derek
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archerdb
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AFNI Message Board
Hello!
I am attempting to conduct multiple regression analyses on my fMRI data and have a few questions.
1) I am conducting two separate multiple regression analysis (each with 1 dependent variable); however, I am actually interested in the difference between these two dependent variables. Is it possible to subtract the beta-coefficient files? Or do I need to do the subtraction before
by
archerdb
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AFNI Message Board
Hi PT,
This looks awesome! Thank you so much.
Derek Archer
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archerdb
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AFNI Message Board
Hi ptaylor,
I emailed you the file. Let me know if there are any issues with it.
Thanks for the help!
Derek
by
archerdb
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AFNI Message Board
Hi ptaylor,
So there were some issues with the origin. I used 3dresample to align the two different images, and I also changed the "Template Space" for my file to TT_N27. If I do 3dinfo to the resulting image, and compare it to brain.nii, the only difference I get is the datum type.
I still can't get this tract to open on top of the image though.
Could the problem be w
by
archerdb
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AFNI Message Board
Hi ptaylor,
Yes, this is what I'm wanting. I just followed your steps, and can open the Walnut Brain. I'm still having issues opening a tract on top of this brain though.
Here are the steps I took to try to get the tract open on this brain:
1) Obtain .nii.gz file in FSL.
2) Use IsoSurface to obtain a .ply file.
--This will open in SUMA in 3D, and the Xhair info s
by
archerdb
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AFNI Message Board
Hi pt,
I can get the TT_N27+tlrc. volume to open with the .ply file; however, I'd like to get a spec file to open with the .ply file as it looks much sharper visually. Maybe I need to make a new spec file? Is there a tutorial to do this? Sorry for being so ignorant on how to do this!
Here is a link showing what I am seeing in SUMA:
Thanks,
Derek
by
archerdb
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AFNI Message Board
Hi pt,
So my command would look like this?
suma -spec N27_both_tlrc.spec -i_ply test_output.ply
When I try this, the .ply file opens, but is not visible. I tried to do the outlined steps to get it to show up, but the "volume redering controls" do not appear for this file. However, when I do:
suma -i_ply test_output.ply
it will open (and is visible), but the volume re
by
archerdb
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AFNI Message Board
Hi pt,
I used the -vol option and it worked! The only problem is that I'd like it to be a 3D brain, instead of 3 different 2D slices. Do I need to run a different line of code for this (with the -sv option?), or am I able to change this in the SUMA viewer somehow?
I'm not sure how the spec file was created, but I can try to recreate one if there are no other options.
Thanks,
by
archerdb
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AFNI Message Board
Thanks for the quick response pt!
I typed in your code, and am getting an error. When trying to open the OUT_PREFIX.ply I get the following error:
You have edges that belong to more than two triangles.
Bad for analysis assuming surface is a 2-manifold.
I am using the following line to open my files:
suma -spec N27_both_tlrc.spec -sv TT_N27+tlrc. -i_ply OUT_PREFIX.ply
An
by
archerdb
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AFNI Message Board
Hello,
I have a 3d ROI (this is a binarized tract from FSL tractography) that I would like to display using SUMA. It is currently a .nii.gz file, and have attempted to use IsoSurface to convert this to a SUMA compatible file using:
Anyone have any experience with this? I've looked through the manual but I couldn't find anything on this.
Thanks,
Derek Archer
by
archerdb
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AFNI Message Board
Hello,
I am attempting to run a simple t-test using diffusoin MRI data. Is it possible to use 3dttest? How would I address the FWE issue?
Thanks,
Derek Archer
by
archerdb
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AFNI Message Board
Hi Gang,
I was looking at the delayed estimates, not the instantaneous ones!
Thanks,
Derek Archer
by
archerdb
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AFNI Message Board
Hi Gang,
I have a few more questions about analyzing the path coefficients for my data. For my specification matrix, I use the following:
A B C D E F G H
A 0 0 0 0 0 0 0 0
B 0 0 0 0 0 0 0 0
C 0 0 0 0 0 NA NA NA
D 0 0 0 0 0 0 0 0
E 0 0 0 0 0 0 0 0
F 0 0 NA 0 0 0 NA NA
G 0 0 NA 0 0 NA 0 NA
H 0 0 NA 0 0 NA NA 0
I use this matrix for two different groups, and I compare the path co
by
archerdb
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AFNI Message Board
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