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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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Pages: 123
Results 31 - 60 of 74
Howdy--
DEGREES OF FREEDOM AIN'T FREE and I'm sick of losing mine to band-passing with regression...but we'd also like to exclude high motion and intensity volumes for processes we run after afni_proc, so perhaps there's a way to have afni_proc run with -regress_RSFC and still generate the motion and intensity censor files--even though no censoring will be done during afni_
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paul.hamilton
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AFNI Message Board
Thanks, Paul! Some juicy bits in there. We'll take @SSwarper for a spin and report back!
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paul.hamilton
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AFNI Message Board
Gentlepeople-
We're in a spring-cleaning / optimization mood over here, particularly with respect to warping and functional-to-anatomical alignment. For each, we'd like to select an option currently in play and compare it to something that might do better. Currently, with respect to warping, we use -tlrc_NL_warp and -tlrc_base MNI152_2009_template.nii.gz, otherwise, vanilla. Is there
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paul.hamilton
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AFNI Message Board
Gents--
My cup runneth over. Thanks.
Rick, SSS (sorry so stupid) but are the contrast coefficients just the simple subtraction of the individual condition betas? If so, 3dcalc will do here but it's very useful know about the flexibility you've implemented in afni_proc.
All best,
Paul
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paul.hamilton
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AFNI Message Board
Gentlepeople of AFNI--
We've run a complete analysis (despike--> volreg-->align-->warp-->regress) on task FMRI data using AFNI proc but forgot one of the subject-level, between-condition contrasts we'd intended to include. To save time, it would be nice to obtain the desired contrast estimates without re-running the entire proc. Can you point us to any existing documentat
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paul.hamilton
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AFNI Message Board
Thanks much, Peter. We'll jump into this and see if something bad happens...
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paul.hamilton
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AFNI Message Board
Hi Peter--
I'll provide one interpretation of Rujing's question in light of something we're also interested in. I think, in this case, Rujing is interested in asking a question about prediction at the group or between-subjects level with resting-state data. There are two ways using 3dsvm that I could see going forward with such a question, one of which you already allude to. Can
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paul.hamilton
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AFNI Message Board
Greetings!
I have an AFNeed that I am unable to provide to myself.
I would like to use align_epi_anat.py to align a not-so-hot blood-perfusion-weighted brain volume to a pretty nice high-res T1. I've tried various permutations of:
cost functions from 3dAllineate large move options the 'edge' approach aligning to the higher contrast labeled or unlabeled scans that are sub
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paul.hamilton
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AFNI Message Board
Greetings, gurujis--
We're having some fun with AFNI's real-time capabilities. So far, we've managed to get motion params and ROI BOLD data and a real-time voxel time-series versus ideal waveform correlation map. Our ultimate objective is to present relatively clean (detrended plus motion, WM, and CSF regressed) ROI data to folks during scanning. Two questions emerge:
1. Can
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paul.hamilton
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AFNI Message Board
Greetings fellow imagers--
The Eklund group showed with resting data that false positive rates are not well contained when traditional assumptions are made about the spatial smoothness of BOLD fMRI data when block-based analyses are conducted--and that this is less so for event-related analyses. This leads us to ask about the implications for resting fMRI connectivity analyses. It's chall
by
paul.hamilton
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AFNI Message Board
Greetings fellow imagers--
The Eklund group showed with resting data that false positive rates are not well contained when traditional assumptions are made about the spatial smoothness of BOLD fMRI data when block-based analyses are conducted--and that this is less so for event-related analyses. This leads us to ask about the implications for resting fMRI connectivity analyses. It's chall
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paul.hamilton
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AFNI Message Board
Hi guys,
Sorry for being both greedy and lazy at the same time but I'm wondering if there is a way to write to disk the results of having run 3dGroupInCorr with a particular seed. Not for publication--just engaging in some quick back and forth with collaborators and thought this would be handy...
Thanks much!
Paul
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paul.hamilton
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AFNI Message Board
Agreed, though, that with the presumably high N of the distributions, a two-sample z test will suffice. Thanks!
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paul.hamilton
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AFNI Message Board
Thanks, Gang. I could see the df being as you say if we assume the voxels are spatially independent but what if there is non-random spatial structure in the data? Wouldn't I be violating assumptions of independence?
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paul.hamilton
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AFNI Message Board
Hi all,
Setting up the problem:
We're using a voxel-wise measure of neural inflammation (NI) to assess depressed and healthy samples. The state of affairs in doing neural inflammation work is such that we do not have strong a priori regional predictions as much as strong general predictions in that we expect to see certain relations hold pretty diffusely throughout grey matter in depre
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paul.hamilton
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AFNI Message Board
I'd say using InstaCalc scratched this itch most effectively...
Thanks, Daniel...
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paul.hamilton
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AFNI Message Board
Thanks much, Daniel! I'll give a try when I'm back at the office tomorrow...
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paul.hamilton
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AFNI Message Board
Hi there, all,
Increasingly, we're generating and using multi-valued, multi-mask volumes for which having the capacity to see masks that fall within a narrow range of values would be desirable. For example, at the moment we're looking at volumes that were generated with a FreeSurfer automatic parcellation process that renders unique numeric labels at all regions parcellated. Values a
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paul.hamilton
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AFNI Message Board
Well, that was easy and it worked perfectly! Thanks, Daniel.
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paul.hamilton
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AFNI Message Board
AFNI Lords,
I have some group level results (warped to TT_N27+tlrc) that I want to examine in the context of the resting-state cortical parcellation by Yeo and colleagues. Description and relevant volumes provided here:
In working with the T1 provided (FSL_MNI152_FreeSurferConformed_1mm.nii.gz) and the liberal 17 network mask (Yeo2011_17Networks_MNI152_FreeSurferConformed1mm.nii.gz) I did
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paul.hamilton
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AFNI Message Board
Hi Gang,
I imagine one of the curses you are faced with in this life is that most psychologists and neuroscientists learn about statistics in terms of within- and between-subjects effects whereas statisticians learn about fixed and random effects--and, worse, that these two distinctions are not analogous.
The most user friendly definitions of fixed and random effects I've seen are here
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paul.hamilton
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AFNI Message Board
Hi Colm,
Just right. Thanks for saving me some time with your (well commented) script!
Paul
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paul.hamilton
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AFNI Message Board
Hi guruji,
I won't bore you with the details about how I got myself into this mess, but I'm wondering if there is a bootstrapping procedure written in AFN-ese? Given the variety of things that require bootstrapping, I wouldn't necessarily expect a full bootstrapping suite or anything, but perhaps a command that could be inserted into a shell script that does the hard part of ran
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paul.hamilton
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AFNI Message Board
Hi all,
Has anyone else seen issues with 3dSeg that appear to be associated with the most recent version of AFNI? For example:
3dSeg -anat MNI152_T1_2mm_brain.nii.gz
results in:
Quote
-- Error SUMA_Class_stats (SUMA_SegFunc.c:5474):
Bad parameters for class CSF
-- Error SUMA_Class_stats (SUMA_SegFunc.c:5474):
Bad parameters for class GM
-- Error SUMA_Class_stats (SUMA_S
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paul.hamilton
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AFNI Message Board
Check this out:
See the Reclamation steps.
I ended up installing wmctrl and then adding the following to my .bash_profile and then running it after afni opens:
alias reclaim='/usr/local/bin/wmctrl -r AFNI -e 0,3644,179,426,387'
Your location parameters may vary...
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paul.hamilton
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AFNI Message Board
Hi Rick,
Quote1. Yes, those bandpassing parameters should be okay. You
are probably using a quadratic or possibly even cubic polort.
Note that using 0.01 instead would probably cost another 4 or
8 regressors.
Okay. Thanks for the affirmation.
Quote2. I agree that it is a lot of regressors to lose, and you
are giving up fewer than most because 0.167 is a bigger
cutoff than most u
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paul.hamilton
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AFNI Message Board
Hi Peter,
Okay...here's the content of the layout file:
***LAYOUT
A geom=+1161+880
A.axialimage geom=337x337+721+541 ifrac=0.8
A.sagittalimage geom=523x217+1725+633 ifrac=0.8
A.coronalimage geom=523x217+1116+605 ifrac=0.8
Thanks for looking and happy to hear thoughts...
Paul
by
paul.hamilton
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AFNI Message Board
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Pages: 123