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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 1 - 21 of 21
Is it possible to pass 3dTtest++ a list as input for setA and setB?
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dk
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AFNI Message Board
Thank you, I will give that a shot. I did misspeak, I am talking about cross-validation not permutation thresholding.
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dk
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AFNI Message Board
I have a big group of subjects, group 1 and group 2. I want to run every possible combination of two-sample t-tests between these two groups. For example, leave one subject out of group 2, keep all of group 1, run two-sample t. Then, leave one out of group 1, leave one out of group 2, run two-sample t, and so on, doing every possible combination.
Is there a pre-built way of doing this in AFNI?
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dk
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AFNI Message Board
I receive the following error when trying to motion-correct, right after the second pass:
Fatal Signal 11 (SIGSEGV) received
fft_shift2
apply_xshear
apply_3shear
THD_rota_vol
mri_3dalign_one
3dvolreg main
Bottom of Debug Stack
I'm not sure what's wrong. The brain is a little bit far forward in the FOV, but other than that, can't think of a
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dk
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AFNI Message Board
Is there any logic in using the -weight option with your brain mask for 3dvolreg? So that only voxels in the mask are used for registration?
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dk
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AFNI Message Board
How do you get 3dDeconvolve to output the non-censored design matrix?
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dk
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AFNI Message Board
I have a project with 4 runs. The regressors seem to show up fine, and there are four sets of two columns (constant, linear drift). The second set of columns (should be constant & linear drift for run 2) are all zeros. I am using a censor, but do not think all of run 2 was censored out. What could cause this?
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dk
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AFNI Message Board
Ah thanks. I don't see where the underlay toggle is, though. And hitting 'u' doesn't do anything.
by
dk
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AFNI Message Board
I need to check co-registration for my images. I know I can overlay one of the images and reduce opacity, but how can I switch between the underlay and overlay (i.e. put the crosshairs on a structure I want to check, and switch between overlay and underlay)?
by
dk
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AFNI Message Board
Sure, let's say I have a script which preprocesses user data with afni_proc.py and then does this:
afni -com "SWITCH_UNDERLAY TT_N27" -com "SWITCH_OVERLAY my_overlay"
3dcalc -a Clust_mask+orig -expr "within(a,2,2)" -prefix roi
I would want to preprocess my data, open AFNI, threshold/clusterize it, save the mask, and have it immediately run my 3dcalc com
by
dk
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AFNI Message Board
I'm trying to integrate AFNI into a shell script pipeline. I want to create a script that will open AFNI with a certain underlay and overlay to check registration, and then once AFNI is closed, the shell script should continue. I've got the opening AFNI with correct underlay and overlay down, however, when I close AFNI, it seems like the terminal hangs so I have to hit control-c to get
by
dk
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AFNI Message Board
When I try and open the draw dset plugin, I get the fatal error:
Fatal Signal 11 (SIGSEGV) received
Atlas_Dset_Name_to_Atlas_Code
Atlas_Name
PLUG_startup_plugin_CB
AFNI:main
Bottom of Debug Stack
I am on an Ubuntu system which already had AFNI installed, but it wasn't installed correctly it seems. I had to add the following lines to my script to see the plugins opti
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dk
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AFNI Message Board
Hey Daniel,
I realized I wasn't doing what I wanted - I need to convert an AFNI ROI into a TurboBrainVoyager .roi file. The TBV file is simply a list of coordinates in native space. So naturally, I'm using 3dmaskdump with the -xyz option to get coordinates. For whatever reason, when I extra raw values from AFNI vs TBV using the converted ROI, I get different values. Makes me believe
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dk
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AFNI Message Board
Forgot I had posted that! Thanks.
As a side question, how do I get the minimum of an inputted 1D array, like this:
1deval -expr 'min(a)' -a tmp__coords'[2]'
I want the minimum of the Y coordinate (column 2 in the text file). Right now it tells me it's an illegal expression.
by
dk
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AFNI Message Board
Hello all,
I am looking for a script of method to convert and AFNI ROI (basically a mask with 0s and 1s) to a Brain Voyager .voi or .roi file. Does anybody know where I can find such a script?
Thanks!
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dk
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AFNI Message Board
I would like to add a regressor and *not* have it convolved with anything. I know I can use stim base, but that won't allow contrasts to be built from the regressor. Is there a way to include a regressor but not have it convolved and still be able to use it in the glmsym?
Thanks
by
dk
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AFNI Message Board
I have 12 subjects I am running 3dttest++ on. When I have all 12 participants, I get the error: "ERROR: Option -setA: ends prematurely after option ___ last participant here ____".
When I remove one particular participant, the error goes away. If I add that participant back, in any order, I get the prematurely ending error again. I am sure there is no typo, and that the participant a
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dk
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AFNI Message Board
When I convert from BRIK to NIFTI, my image is no longer in the correct orientation, and doing 3drefit on the .nii.gz file itself does nothing. Any suggestions on fixing this?
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dk
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AFNI Message Board
I have a .ROI file from BrainVoyager, which is simply a list of coordinates in BrainVoyager native space. I would like to create an ROI in AFNI using this list of coordinates.
How would I do such a thing? The list looks something like:
40 61 8
28 60 8
29 60 8
37 60 8
40 60 8
41 60 8
42 60 8
In order of X, Y
by
dk
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AFNI Message Board