Show all posts by user
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
Hi Rick,
rick reynolds Wrote:
-------------------------------------------------------
> Ziad has now left the country for a bit (clearly
> just
> to avoid your post).
clearly
> While I do not know all of the cases to consider,
> you
> can at least override the conversion upon write
> by
> claiming to want GIFTI as RAI (maybe AS_IS would
> be a
>
by
nick
-
AFNI Message Board
Hi Ziad et al,
here a friendly reminder for this question.
cheers,
Nick
by
nick
-
AFNI Message Board
Hi Emily,
Emily Wrote:
-------------------------------------------------------
>
> I would like to perform an FDR correction on the
> ANOVA results (q value=0.05). However, the
> smallest qvalue I can get on the afni gui is
> .2920. Does this simply mean that none of the
> voxels would survive that type of correction,
Most likely.
(Not that I would recommend u
by
nick
-
AFNI Message Board
Dear Ziad et al,
Here a follow-up question re the coordinate change in GIFTI [1].
Using a new version of AFNI [2] I want to convert .asc surfaces generated by @SUMA_Make_Spec_FS (and resampled using MapIcosahedron) to GIFTI.
I observed that the .asc surfaces are in LPI coordinates. However ConvertSurfaces seems to swap signs of x and y coordinates when going from .asc to GIFTI.
Is it
by
nick
-
AFNI Message Board
TheChymera Wrote:
-------------------------------------------------------
> Ok, sorry, now I notice there is a file called
> "afni" - but how will I get it to launch? it keeps
> saying permission denied, and chmod -x afni won't
> do anything about it.
chmod a+rx afni
followed by
./afni
?
by
nick
-
AFNI Message Board
Aaron Wrote:
-------------------------------------------------------
> I have been doing some quality checks on our fMRI
> scans and I have been noticing a bright (high
> intensity) band of activation that is consistently
> in the top 1-2 most superior slices. This is
> happening in many of our scans. Does anyone know
> what could be causing this
That sounds pretty no
by
nick
-
AFNI Message Board
Emily Wrote:
-------------------------------------------------------
> I am trying to run a mixed model ANOVA with Group
> (Depressed, Control) as the between subject
> variable and Mood Induction Condition as the
> within subjects variable (Rumination,
> Distraction).
Have you considered using 3dttest++ instead? That may make the results easier to interpret as you keep t
by
nick
-
AFNI Message Board
Sid Sarinopoulos Wrote:
-------------------------------------------------------
> But, the timeseries data that I use for these
> calculations presumably still contain temporal
> signal drift, some motion effects, etc.
>
> So, my question is, can we get 3dDeconvolve to
> write out the timeseries data after all the
> undesirable stuff has been regresses out? Or, is
by
nick
-
AFNI Message Board
lcnature Wrote:
-------------------------------------------------------
>
> BTW, my build of AFNI and SUMA are still the June
> version this year (sorry I am not using the most
> updated version because I already had a bunch of
> downstream analysis codes that used result from
> old SUMA and I am not sure if updating SUMA will
> mess up anything due to the coordinate
by
nick
-
AFNI Message Board
Sid Sarinopoulos Wrote:
-------------------------------------------------------
> I wonder if you can help me with this one.
> I need to analyze data, in original space, for a
> slow event-related study with fixed 35-s ITIs.
> I need (1) to use preprocessing steps and GLM
> analysis to identify ROIs
> But then, also using those ROIs for masks, I would
> like to (2) e
by
nick
-
AFNI Message Board
Isaac Schwabacher Wrote:
-------------------------------------------------------
> Hi Gurus,
>
> Since there doesn't seem to be a MATLAB function
> to convert from BRICK_STATAUX to a more
> human-readable format,
There is BrikInfo_2_niml_writesimple that makes it a bit more readable...
> I think it would be nice if
> the FUNC_*_TYPE macros from 3ddata.h cou
by
nick
-
AFNI Message Board
Hi Mingbo
lcnature Wrote:
-------------------------------------------------------
> Ha Nick, I mistakenly thought it was Bob
> responding to my last post.
I'll take that as a compliment... mostly
> How do you feel about
> the python package?
I haven't tried it yet. It's on my list, but so are many other things.
best,
Nick
by
nick
-
AFNI Message Board
Hi Gang,
Gang Wrote:
-------------------------------------------------------
> > To get a firmer grasp on this I played a bit
> with the effect of scaling when adding effects
> > of different sizes to the data [...]
> > Do you think this is a valid simulation and
> would that mean that the sos normalization would
> be
> > sufficiently valid (although a
by
nick
-
AFNI Message Board
lcnature Wrote:
-------------------------------------------------------
> I am wondering what is the best command to
> deconvolve the signal to different conditions, but
> assuming they share the same hemodynamic response
> function. It is similar to IM, allowing HRF to
> vary between voxels (fixed for each voxel), but
> estimating beta only for each condition, instead
&
by
nick
-
AFNI Message Board
Gang Wrote:
-------------------------------------------------------
> > But if I understand you correctly that approach
> is fine, no?
>
> Well, not so obvious to me. The voxel-wise scaling
> by sqrt(SOS) is definitely different between your
> 'within-subject' vs 'between-subject' maps, and
> that means the scaling would change the pairwise
&
by
nick
-
AFNI Message Board
Hi Gang,
Gang Wrote:
-------------------------------------------------------
> > I am not sure whether after scaling by the
> square root of sos they follow a t-distribution...
> should they?
>
> Presumably they should follow a t-distribution by
> a factor, something like sqrt(n(n-1)).
I see. So then I would be running a t-test on values following a t-distribut
by
nick
-
AFNI Message Board
ziad Wrote:
-------------------------------------------------------
> You make a good point, this should be fixed
> properly. I just went over the necessary changes
> this with Rick and we should have something ready
> in the next few days. GIFTI surfaces produced by
> SUMA will be LPI.
For those who may find this post in the future: this issue is now resolved thanks to Zi
by
nick
-
AFNI Message Board
Hi Ziad,
ziad Wrote:
-------------------------------------------------------
> In SUMA versions postdating this message GIFTI
> surfaces will be assumed to be in LPI, rather than
> RAI, in keeping with the GIFTI standard.
great! Many thanks for implementing this change.
I just tried it out and the overlay is perfect now - with the canonical xform matrix (identity).
> A
by
nick
-
AFNI Message Board
Hi Gang,
Gang Wrote:
-------------------------------------------------------
> Your wording of within- vs. between-maps confused
> me quite a bit before. Thanks for the
> clarifications.
Apologies for the confusion.
> > A direct comparison with 3dttest++ with -setA,
> setB and -paired gives a lot
> > of blobs for the within>between just because it
> h
by
nick
-
AFNI Message Board
Hi Gang,
Gang Wrote:
-------------------------------------------------------
> > Looking at the between- and within- maps
> separately (computed using 3dttest++ with -setA),
> > the distribution of t-statistics seem quite
> similar.
>
> I'm lost at your description. You have the
> correlation coefficients (transferred z-scores for
> group analysis)
by
nick
-
AFNI Message Board
Dear AFNI experts,
I'm doing multivariate pattern analysis and computing both within- and between-subject correlation-differences for group analysis. Individual subject maps have a mean of zero and unknown variance under the null hypothesis. Correlations were fisher-transformed before computing differences to make them more 'normal'.
Looking at the between- and within- maps s
by
nick
-
AFNI Message Board
Hi Ziad,
ziad Wrote:
-------------------------------------------------------
> You make a good point, this should be fixed
> properly. I just went over the necessary changes
> this with Rick and we should have something ready
> in the next few days. GIFTI surfaces produced by
> SUMA will be LPI.
That's great, many thanks for making these fixes!
Also I changed th
by
nick
-
AFNI Message Board
ziad Wrote:
> nick Wrote:
> > ziad Wrote:
> > > Problem solved, I hope. The gifti coordinates
> > > transform was being applied after center of
> > mass
> > > computation. The next set of binaries will
> > contain
> > > the fix.
> >
> > Thanks for making this fix - I will give it a
> try
> > once the new bi
by
nick
-
AFNI Message Board
Hi Ziad,
ziad Wrote:
-------------------------------------------------------
> Problem solved, I hope. The gifti coordinates
> transform was being applied after center of mass
> computation. The next set of binaries will contain
> the fix.
Thanks for making this fix - I will give it a try once the new binaries are there.
Does that mean I should set the xform matrix m for
by
nick
-
AFNI Message Board
Hi Ziad,
thanks for your reply.
ziad Wrote:
-------------------------------------------------------
> It does look like there is an LPI/RAI problem here
> but I am not sure where it is getting introduced.
> I do use GIFTI versions of FreeSurfer surfaces
> fine so there has to be something else going on
> here.
FYI, the GIFTI surface I use were generated using python
by
nick
-
AFNI Message Board
Hi Ziad,
welcome back on the message board
Here a friendly reminder for this post.
best,
Nick
by
nick
-
AFNI Message Board
paranoidandroid Wrote:
-------------------------------------------------------
> But one important question: Does this also allow
> negative beta values for the individual functions?
> Because I am expecting negative BOLD components in
> my HRF.
Yes, TENTs allows for get negative beta values.
by
nick
-
AFNI Message Board
SarahT Wrote:
-------------------------------------------------------
> I've completed analyzing my data and now have a
> few significant surface clusters (using SurfClust,
> projected onto an average brain with standardized
> spherical mesh) for my contrasts of interest. In
> pre-processing and running single subject analysis
> in the volume I kept the data in its o
by
nick
-
AFNI Message Board
Jake Wrote:
-------------------------------------------------------
> I have the images in NIFTI format [...]
> I'm just having
> problems creating the dataset.
AFNI is be able to read (and write) NIFTI images. Did you 'cd' to the directory where the nifti files are and open the AFNI viewer from there?
If you really want 'AFNI' format (.HEAD and .BRIK[.
by
nick
-
AFNI Message Board