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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
Page 9 of 9
Pages: 56789
Results 241 - 270 of 270
ziad Wrote:
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> Hi Nick,
> >
> > A few steps to illustrate the issue:
> > 1) suma start-up: AHNF=0
> > 2) ctrl-click on surface node 48: AHNF=48
> > 3) mouse-over on AHNF: AHNF=48
> > 4) mouse leaving AHNF (without click or
> keyboard
> > input): AHNF=0
> I don't get this beha
by
nick
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AFNI Message Board
ziad Wrote:
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> > > And it works wonderfully
>
> > Sorry, I didn't notice this before, but it
> seems
> > that with Pls1 it sets overlay and threshold to
> > sub-briks k and k+1, respectively, rather than
> 2*k
> > and 2*k+1. Would it be much work to implement
> the
> > latt
by
nick
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AFNI Message Board
Hi Ziad,
nick Wrote:
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> Hi Ziad,
>
> ziad Wrote:
> --------------------------------------------------
> -----
> > > selected as overlay. As I mentioned earlier
> it
> > > would be particularly nice - but not of
> highest
> > > priority - that if IxT is set to Pls1,
> > sele
by
nick
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AFNI Message Board
Hi Ziad,
ziad Wrote:
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> > As far as I can tell, however, it does not
> allow
> > for setting the sub-brik based on the node
> > selected. I tried both first-button and
> > third-button click, both with and without
> > ctrl+shift modifiers, but that did not work.
>
> I forgot about that part.
by
nick
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AFNI Message Board
Colm Connolly Wrote:
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> I know in the grand
> scheme of things that 0.005 may not make a huge
> difference,
Indeed, it really does not. Many other factors in your processing pipeline will have a larger effect on which clusters survive after cluster-based thresholding.
> but I'd still like to know whether
> 3dCl
by
nick
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AFNI Message Board
kentman234 Wrote:
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> nick Wrote:
> --------------------------------------------------
> -----
> > kentman234 Wrote:
> > > - I want to go data-driven. That's why I
> > mentioned
> > > ICA, to descriminate the components of the
> two
> > > classes i.e. one component should indica
by
nick
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AFNI Message Board
Dear Ziad,
ziad Wrote:
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> So I have something that should do the trick. I
> don't know if I will get the binaries in by
> Monday, but Tuesday at the latest should have the
> new additions.
>
> Basically, for large numbers of sub-bricks, the
> menu choosers in AFNI change into what we call
> arrow head
by
nick
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AFNI Message Board
Dear AFNI experts (particularly, Ziad),
I'm viewing data using the SUMA dot product feature, but it crashes frequently as soon as I press 'D' (after loading a dataset of course). I've tried to vary the size of the number of time points and subjectively it seems particularly prone to crashing for datasets with many time points; with more than 50 time points it always crashes
by
nick
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AFNI Message Board
kentman234 Wrote:
> - I want to go data-driven. That's why I mentioned
> ICA, to descriminate the components of the two
> classes i.e. one component should indicate a
> unique class. You said that this is not possible
I said I did not see how that could work - feel free to prove me wrong, that means I would have learnt something interesting.
Re your other questions:
by
nick
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AFNI Message Board
tesslermh Wrote:
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> I'd like to know how to do the surface equivalent
> of drawing a sphere on a volume.
Does this post answer your question?
best,
Nick
by
nick
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AFNI Message Board
> kentman234 Wrote:
> Although there are many things that must be further understood, in my opinion, the plan of the project should be more specified
> theoretically
This all depends on your research question. Are you interested in finding which brain regions can dissociate between different times of movies? In similarities of differences of time-courses in different regions? Lo
by
nick
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AFNI Message Board
Michael Amlung Wrote:
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> We're using AlphaSim to estimate a cluster extent
> threshold for our group maps, and a reviewer for
> one of our articles suggested that we must used
> 3dFWHMx to estimate the true smoothness in X, Y,
> and Z rather than just putting the size of the
> blur we applied to the data (using t
by
nick
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AFNI Message Board
kentman234 Wrote:
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> After I did ICA to the data of one subject, i got
> 25 components (ICs). Now i need to work on the
> time courses file which is of HDR format. This
> file contains the time courses o fthe 25
> components. How can afni read this file?
I assume you have not only HDR but als IMG files - the former is
by
nick
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AFNI Message Board
Anita Cservenka Wrote:
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> Hi AFNI gurus,
>
> I'm trying to do a 2x2 analysis on a longitudinal
> dataset in which I have two groups (let's call
> them group A and group B). Each group has 4
> participants, and each of these participants has a
> baseline fMRI scan and a follow-up fMRI scan.
Ouch, 4 pa
by
nick
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AFNI Message Board
Inbal S.L. Wrote:
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> Hello.
> I wanted to create a time series data for a
> selected set of voxels.
> I have the PRI coordinates for a list of the
> voxels I am interested at, and a time series data
> vector for each one of those voxels.
You can use AFNI_XYZcontinuous2Index and it's inverse, AFNI_Index2XYZco
by
nick
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AFNI Message Board
kentman234 Wrote:
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> I want to do a project about classification of
> fMRI data. I have data for 20 subjects who see two
> types of videos. The data have been already
> preprocessed
How exactly? Do you have different predictors for the two types of movies in a GLM?
Multiple exemplars for each type or just one? Are you us
by
nick
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AFNI Message Board
giacomo handjaras Wrote:
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> Hi to All!
> Is there a function in the matlab library that do
> the same thing of "clusterize" in the graphichal
> interface (i.e. clustering using a threshold and a
> minmum cluster size)?
> How can i do that in matlab?
We have a toolbox that should do it, available from surf
by
nick
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AFNI Message Board
rwcox Wrote:
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> AFNI's blurring programs (3dmerge and
> 3dBlurInMask) just add smoothness to
> datasets, so if there is some pre-existing
> smoothness, you will end up with more smoothness
> than you might anticipate. I imagine that SPM
> (etc.) does the same.
Yes, that's what I assume as well.
Pleas
by
nick
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AFNI Message Board
Hi Rick,
thanks for your reply;
rick reynolds Wrote:
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> Smoothing is done via some algorithm that is only
> going to be
> approximate because it is over discrete space.
> How a program
> author decides to deal with that will certainly
> have an effect.
I think I understand that - it makes sense.
> So
by
nick
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AFNI Message Board
Hang Joon Jo Wrote:
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> Actually, I don't know anything about SPM, but
> just for your information, there is an AFNI
> program named "3dBlurToFWHM". It iteratively blurs
> little bit to a target FWHM.
thanks for noting this. I have used this program in the past, and it's a handy tool.
> It might b
by
nick
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AFNI Message Board
Dear AFNI gurus,
I've done a simple comparison between 3dmerge smoothing and spm_smooth and get somewhat different results, namely that for smaller smoothing kernels the (estimated) smoothness is lower with spm_smooth than in AFNI, while both programs seem to smooth the data a bit too much (that is, as estimated by 3dFWHMx).
I've generated random volume data in matlab (with randn)
by
nick
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AFNI Message Board
Juan W Wrote:
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> I am trying to do small volume correction via
> AFNI. I googled but just find some methods for
> this analysis via SPM5. Anyone ever used AFNI to
> process this? I am only some familiar with AFNI.
This would work similar as for whole-brain correction:
- run the GLM for each participant and save the resid
by
nick
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AFNI Message Board
> Does this mean one should NOT model fixation with
> a separate regressor? I have run 3dDeconvolve with
> and without modeling fixation, and this seems to
> change my data quite a bit.
Indeed, people generally do not model fixation with a separate regressor, but rather consider the fixation as an implicit baseline to which the other conditions of interest are being compared.
by
nick
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AFNI Message Board
John Risman Wrote:
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> Hello all,
>
> I'm having the following problem using the
> local_time format with 3dDconvolve. For some
> subjects, some runs have zero events of a
> particular type. So, I am not sure how to code
> that when the times for different runs are in
> different rows.... Is there a speci
by
nick
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AFNI Message Board
Hi Ziad,
just a little reminder - if you would have the possibility to implement this feature that would be great.
thanks,
Nick
by
nick
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AFNI Message Board
Hi Ziad,
sounds good. Hope you have a good time in China!
cheers,
Nick
by
nick
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AFNI Message Board
Dear Ziad (and other AFNI gurus),
I've started working with big datasets in SUMA, big in the sense of the number of 'time points' (in quotes, because these are actually values from MVPA analyses). We're talking about relatively low resolution surfaces (~10,000 nodes) with currently about 10,000 time points, aiming for more time points in future analyses.
The 'dot pr
by
nick
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AFNI Message Board
Hi Yiyu,
consider the matlab code included below. It has three parameters: the input filenames for the pial and white matter surfaces (.asc), and the output filename (usually .1D is used). You can load the output file in SUMA.
hope this helps,
Nick
function thickness=cortical_thickness(fn_white,fn_pial,fn_out_thickness)
white_coords=read_surf_coords(fn_white);
pial_coords=read_sur
by
nick
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AFNI Message Board
Dear AFNI experts,
recently I've started using SUMA to view two hemispheres together. This works very nicely with 3dGroupInCorr, especially with inflated hemispheres (using a customly made .spec file and surfaces).
I run into a few issues however:
1) I can't figure out how to load data for two surfaces. The 'load dset' option only loads data for the first (left) hemis
by
nick
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AFNI Message Board
Page 9 of 9
Pages: 56789