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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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I changed the stim file times to local_times and changed the parameter in the 3ddeconvolve script and everything is fine!
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AFNI Message Board
Ok, so I realised my stim event files needed to have as many rows as runs with a * to indicate if there were none of that stim class in that run.
With that changed, my DM has slightly (attached). But it still eems as if something is going wrong with interpreting the timings in the runs, for example i get these warnings when running 3dDeconvolve:
++ Auto-catenated input datasets treated as
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AFNI Message Board
Hi, I'm running a traditional (not gPPI) PPI analysis using 3dDeconvolve. I want to do this across four runs per subject, so I am trying to concatenate all runs in time by inputting them all into 3dDeconvolve at once, but the design matrix i get out is not what i expected. Could someone tell me what I'm doing wrong?
my 3dDeconvolve script is as follows for one subject and their four
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AFNI Message Board
Hey
Thanks! This is great, and I think we're getting closer, but it's still not quite what I'm after.
My resulting DSET_MAP_IN_CLUST now has the same number of voxels as the original cluster (great) and the large cluster is now split into the ROIs as I'd hoped (i.e. voxels are now different values across each of these regions, e.g. 1 in Region 1, 2 in region 2....). The
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AFNI Message Board
Sorry that should say the total number of voxels should stay the same. When I've parcellated with atlas maps, the total number of voxels across all resulting clusters changes from the total voxels in just the one large cluster
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AFNI Message Board
I have a cluster of over 1000 voxels found using 3dClusterize, but it straddles various functionally independent regions. Is there any way I can split this cluster into a smaller number of clusters based on their region using AFNI or 3dClusterize in such a way that the number of clusters would remain the same as the number of clusters in the original large cluster? thnx
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AFNI Message Board
Found a solution, I just subtracted 0.95 from each voxel using 3dcalc and then set the upper bound to 0.05 with pos unchecked on the GUI
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AFNI Message Board
Hey y'all,
I'm trying to edit the range of the intensity bar in the afni viewer. Specifically I'd like to raise the lower bound from 0 to 0.95, and keep the higher bound at 1. Thus far it seems it's only possible to change the higher bound.
I read that the lower bound is automatically set at the minimum voxel value in the map. If I cannot change this, how can I remove al
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AFNI Message Board
I'm trying to convert a ROI mask i've downloaded to MNI space but am having a lot of difficulty.
The file is an .hdr file and this is the output from 3dinfo:
Dataset File: superior_temporal_sulcus_posterior_branch_R.img
Identifier Code: ANZ_Y-maODBW7WtxIxcckBBIGA Creation Date: Fri Nov 1 16:43:40 2019
Template Space:
Dataset Type: MRI Anatomy (-anat)
Byte Order:
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AFNI Message Board
I'm sorry I don't quite understand, actually. I am not familiar with this notation for t-tests: does (A1B1-A2B1)-(A1B2-A2B2), for example, mean I do the subtraction of A1B1-A2B1 and the subtraction A1B2-A2B2 for each subject and the run a paired sample t-test between the resultant maps? Or do I need to run ttests instead of subtractions? I'm unsure how it could be the latter, since
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AFNI Message Board
I am trying to run a repeat measures 2x2 anova and correct for multiple comparisons all in one, a la 3dttest++ -ClustSim. Is there any functionality to do this yet? I am using 3dANOVA3 to run the anova.
If not, which method is best for permutation testing to correct for multiple comparisons in a repeat measure 2x2 ANOVA in afni?
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AFNI Message Board
Sorry the link isnt working and im unclear on how to get r values from 3dttest++, could you please clarify?
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AFNI Message Board