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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
Naveed Wrote:
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> Yes u r right, I got better smoothness with
> 3dmerge
I'm not sure if "better" is the most appropriate word here, but larger values using 3dmerge make sense.
by
nick
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AFNI Message Board
yfh2013 Wrote:
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> I want to know how can I modify the
> All_lh_ld141.spec( in the demo script
> run_stdmesh_demo ) from the demo data to fit my
> own surface
Just open the file in a text editor. Each surface specified starts with a aline containing 'NewSurface', followed by a series of lines in the form "k
by
nick
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AFNI Message Board
Hi Ziad,
ziad Wrote:
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> This is certainly possible, but not having touched
> ToyTalk in ages, I am not actually sure how
> reliable it still is.
> At the moment, the ToyTalk implementation is
> mostly matlab code that duplicates some of what is
> done in the C-api that AFNI/SUMA use. I am
> wondering if we sho
by
nick
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AFNI Message Board
Dear all (notably, Ziad),
the ToyTalk function in the AFNI matlab library provides a nice example on how matlab can receive data from SUMA over NIML. However, I would be interested in more sophisticated visualization. In particular I would like to be able to visualize data in overlays, as well as data that formed the basis of such overlays, in matlab, interactively while clicking around in SUM
by
nick
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AFNI Message Board
yfh2013 Wrote:
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> Dear Sir,
> I have translated the freesurfer result to the
> SUMA by using @SUMA_Make_Spec_FS. Now I want all
> the subjects to align to a Standard-Mesh Surfaces.
> My question is as followed:
> 1. If I need to use MapIcosahedron to produce
> the Standard-Mesh Surfaces for every subject or
by
nick
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AFNI Message Board
Naveed Wrote:
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> Is this function works similar to this command>>
>
> $
> 3dBlurToFWHM -FWHM 10 -automask -prefix
> conn_smooth -input Connectivity_mask_anat+tlrc
Almost always the input data already has some smoothness, in which case they are not identical:
- 3dBlurToFWHM smooths the data *until* it has reache
by
nick
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AFNI Message Board
Hi Daniel,
Daniel Glen Wrote:
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> MNI and
> Talaiarach are "spaces", not coordinate orders, so
> locations within either can be expressed in any of
> the 27 potential variants of coordinate order
I thought there were 48 variants - 3! * 2^3. Does that make sense?
Nick
by
nick
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AFNI Message Board
Naveed Wrote:
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> I have acquired the seed based connectivity
> result, but it looks to sparse.
> Can anyone suggest me the command to smoothen the
> AFNI volume file.
try 3dmerge; example #1 in the help should get you started.
by
nick
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AFNI Message Board
Omar Maximo Wrote:
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> > To be clear, you seem to be describing a paired
> > t-test here. Did you run 3dttest++ with the
> > -paired option?
>
> I think I should have started from here. On my
> 3ddeconvolve script for each participant, I had 4
> trials with their respective timing information.
> Then
by
nick
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AFNI Message Board
Omar Maximo Wrote:
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> I had a quick (or maybe even dumb) question
> regarding group analysis on AFNI. Let's say I have
> 2 trials, A and B, and 2 groups, control and
> clinical (let's say autism). I made a contrast A
> vs. B on each group and when I look at the results
> on each group, A condition will be in
by
nick
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AFNI Message Board
PeterKohler Wrote:
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> nick Wrote:
> --------------------------------------------------
> -----
> > I don't understand this question.
> > freesurfer_read_surf returns vertices and face
> > indices of a surface, which is not much related
> to
> > ROI work. Except of course that the indices in
&
by
nick
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AFNI Message Board
PeterKohler Wrote:
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> Hello AFNI Gurus,
>
> I am trying to use Matlab to determine which
> vertices of a Freesurfer surface are included in a
> few surface ROIs that I have created in SUMA. I
> load the Freesurfer surface into Matlab like
> this:FSv =
> freesurfer_read_surf('lh.pial');
> I have t
by
nick
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AFNI Message Board
swijeakumar Wrote:
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> How do I calculate the residual variance as a
> result of an individual-based Deconvolution
> (3dDeconvolve). the file obtained from using the
> -errts option provides the residual variance as a
> function of time, correct?
No, it contains the residual at each time point.
See ; epsilon_i is th
by
nick
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AFNI Message Board
jason-avery Wrote:
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> Hi, I'm trying to figure out the answer to a
> couple of questions I've had for a while now. I've
> been analyzing data on the cortical surface using
> a standardized mesh of -ld (linear division) of
> 125.
> My first question is:
> What is the actual grid size of this standa
by
nick
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AFNI Message Board
rmruczek Wrote:
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> To reiterate, we have data collected from a
> 32-channel coil. So the EPI has very high SNR at
> the surface, falling off toward the center of the
> brain. Because of this, I am finding it difficult
> to judge the EPI-anat alignment, because I can't
> threshold the EPI in a way that highlight
by
nick
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AFNI Message Board
Hi Zaid,
ziad Wrote:
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> The problem was caused by a recent change I had
> made in an effort to save some CPU time under
> certain conditions. I will check the repair in
> sometime tomorrow and binaries should be rear to
> go tomorrow (Tuesday March 4th) evening.
Got it, and it works again - using Version AFNI_2011_
by
nick
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AFNI Message Board
Hi Ziad,
ziad Wrote:
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> The problem was caused by a recent change I had
> made in an effort to save some CPU time under
> certain conditions. I will check the repair in
> sometime tomorrow and binaries should be rear to
> go tomorrow (Tuesday March 4th) evening.
thanks for looking into this, and I look forward to t
by
nick
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AFNI Message Board
nick Wrote:
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> for some odd reason using the dot product mode in
> SUMA stopped working with the latest AFNI.
>
> I get the following message:
>
> ++ Notice SUMA_D_Key (SUMA_input.c:1307
> @17:26:01):
> No contralateral dset
> Error SUMA_Set_Sub_String (suma_utils.c:3607):
> NULL input
> War
by
nick
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AFNI Message Board
Dear all (in particular, Ziad),
for some odd reason using the dot product mode in SUMA stopped working with the latest AFNI.
I get the following message:
++ Notice SUMA_D_Key (SUMA_input.c:1307 @17:26:01):
No contralateral dset
Error SUMA_Set_Sub_String (suma_utils.c:3607):
NULL input
Warning SUMA_AddDsetNodeIndexColAttr:
Failed to set substring for COLMS_LABS at 0
++ Noti
by
nick
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AFNI Message Board
Hi Kara,
kblacker Wrote:
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> Thanks for the explanation of the node index
> values; that was very helpful.
You're welcome.
> However, when I set
> the pad_to_node value as you suggested I am still
> getting the same error message. One thing that
> occurred to me is that my input data for
> ConvertDset
by
nick
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AFNI Message Board
Hi Kara,
kblacker Wrote:
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> I tried to use
> ConvertDsets as you suggested but I am getting an
> error that I can't figure out. Below is my script
> and the error message:
>
> Script:
> foreach subj ( p01 p02 p03 p04 p05 p06 p07 p08 p10
> p11 p14 p15 p16 )
> cd /Volumes/KaraData/fSIR/$subj/$subj.r
by
nick
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AFNI Message Board
kblacker Wrote:
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> At
> this point, I have created surface models using FS
> and run @SUMA_Make_Spec_FS (which I understand
> from the handouts is the point at which my
> standard meshes are created, correct?). I have run
> preprocessing using afni_proc with the surf block
> included. I structured my afni_proc off
by
nick
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AFNI Message Board
jgray7700 Wrote:
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> I am trying to run 3dDeconvolve for the first time
> without having used waver first. […] I am making
> the start times when the stimulus is presented and
> the end time is the start time + reaction time.[…]
> I get the following error after trying to
> run:
>
> 3dDeconvolve -input pb04.$
by
nick
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AFNI Message Board
nnavolio Wrote:
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> I'm not sure how transforming to z-scores fixes my
> problem. The voxels outside the brain end up with
> 0% accuracy. If I convert to z score, wouldn't
> that just end up with a very negative z-score at
> those voxels?
My suggestion was to convert the p-values of your classification accur
by
nick
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AFNI Message Board
nnavolio Wrote:
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> We are doing
> the following steps to perform and then threshold
> an MVPA […]
>
> -run classifier in subject space
> -bring the accuracy maps for each subject into
> stereotactic space (using @auto_tlrc for anat,
> then align_epi_anat.py)
> -performing a parametric group analysis (e.g.
by
nick
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AFNI Message Board
jdviviano Wrote:
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> We are attempting to analyze a mixed effect/block
> design with 3dDeconvolve and are finding some
> strange things. When we contrast our condition
> events with control events, we obtain positive
> contrasts, but when we contrast the same
> condition's blocks with control blocks, we obtain
&g
by
nick
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AFNI Message Board
ziad Wrote:
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> There are no tools to do this at the moment.
> However one way to do this is to consider a
> standard mesh with a low number of subdivisions.
> For instance, if you want about 4000 nodes over
> the whole hemisphere, you can create standard
> meshes with ld20 and then use the nodes from the
> low res
by
nick
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AFNI Message Board
chpiero Wrote:
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> is it possible to export a correlation matrix
> (HEAD BRIK) in a txt matrix?
A correlation matrix is not the same as "HEAD BRIK". "HEAD" and "BRIK" are the extensions of AFNI header and data volumetric, respectively. The HEAD file contains meta-information about the data (such as v
by
nick
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AFNI Message Board
tsliu Wrote:
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> 1. When you say "You should also consider
> computing %signal change etc. AFTER you have
> mapped the time series onto the surface and
> smoothed those time series on the surface, rather
> than in the volume." Do you mean this is a better
> method than compute % signal and then warp to
>
by
nick
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AFNI Message Board
Kai Wrote:
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> Can I use 3dUnifize for surface creation?
No, it's intended to uniformize white matter intensity.
My favorite program to generate surfaces is FreeSurfer's recon-all; an alternative is Caret.
by
nick
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AFNI Message Board