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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
maitra Wrote:
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> Could someone please tell me how to cite AFNI (ie
> provide the bibliographic reference) in a
> publication?
Google is your friend; the first hit for "how to cite afni" gives:
by
nick
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AFNI Message Board
Isaac Schwabacher Wrote:
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> No, but that's not the problem. The issue is when
> you use that result to index into the array:[...]
Right, as you illustrated (and mentioned earlier) there is a base0 versus base1 indexing.
So all is good; the coordinates reported by the OP were (68, 33, 52) versus (68, 32, 51), but it escape
by
nick
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AFNI Message Board
Isaac Schwabacher Wrote:
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> No, I mean that if you go to the voxel that MATLAB
> says is (68, 33, 52), then MATLAB will say that
> that voxel's global index in the dataset is
> 372560. If you navigate to the same voxel (i.e.,
> the same location in the dataset) in AFNI, the
> global index will be 372559 and the
by
nick
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AFNI Message Board
Isaac Schwabacher Wrote:
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> I was confused by that at first, too, but the
> first indices match because the global index is
> also off by one.
I am stil confused then, because you wrote "the MATLAB voxel is at (68, 33, 52) while the AFNI voxel is at (67, 32, 51). "
Did you mean (67, 33, 52) for the MATLAB voxel?
by
nick
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AFNI Message Board
Isaac Schwabacher Wrote:
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> The issue is that MATLAB indices start at 1, while
> AFNI indices start at 0. So when addressing the
> entire brick with a single index, MATLAB index
> 372560 is the same voxel as AFNI index 372559, and
> the MATLAB voxel is at (68, 33, 52) while the AFNI
> voxel is at (67, 32, 51).
I
by
nick
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AFNI Message Board
kickan Wrote:
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> Is there an AFNI function that can apply a certain
> threshold (e.g. p = 0.01, uncorrected) to a
> statistical image and then report the number of
> voxels in each cluster that survives the voxel
> threshold?
There is: 3dclust.
by
nick
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AFNI Message Board
pstchan Wrote:
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> When I apply '3dAllineate' or 'align_epi_anat.py'
> to align a T1 anatomical dataset, I find a
> difference in the output for the same input
> dataset in NIFTI and BRIK format
AFNI can store additional transformations in the fields
- ALLINEATE_MATVEC_B2S_000000
- ALLINEATE_MATVEC
by
nick
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AFNI Message Board
kickan Wrote:
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> I have used 3dttest++ for a group analysis and
> would like to get p-values for each cluster. For
> the first level analysis, the smoothness is first
> estimated from the residuals, and 3dClustSim is
> then used with this estimate. What should I use to
> estimate the smoothness for the group analysis?
by
nick
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AFNI Message Board
tobiamj Wrote:
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> after generating both lh and rh
> surfaces in SUMA, is there a way to reorder the
> nodes of the right hemisphere to match the anatomy
> of the left hemi?
There is a function in PyMVPA that can compute such a mapping. The function is get_sphere_left_right_mapping in mvpa2.support.nibabel.surf.
by
nick
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AFNI Message Board
Jeremy Wrote:
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> Hi everyone!
> Normalize: 3dcalc -gscale -datum float -prefix
> func_normalized -a func_+orig -b mean+orig -expr
> "a/b*100"
> The normalize I mean is to let the functional
> data to divide the mean value of themselves.
> I want to know if it is necessary to do it so
> that eve
by
nick
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AFNI Message Board
Danny Wrote:
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> I was wondering if there is a "best" point during
> preprocessing to do the registration to a standard
> template? I know some programs do it before
> subject-level statistics, while others do it
> after.
>
> I am currently running everything within
> AFNI_proc.py. I am wondering if
by
nick
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AFNI Message Board
Emperor Zhark Wrote:
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> It was 20 years ago, in early July 1994, that I
> started work on AFNI.
Happy anniversary, and many thanks to the whole crew for the great work on AFNI!
by
nick
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AFNI Message Board
Nilufar Wrote:
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> I am trying to use afni's MATLAB library to read
> and write surface data in .niml.dset format.
> Using 3dVoltoSurf, I converted volumetric data to
> surface data. Now, when I use this command in
> matlab:
> fn = 'surf_lh.niml.dset' %my surface data
> this error occurs:
> %%%%%
by
nick
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AFNI Message Board
lzhyoung Wrote:
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> I am confused about the update of the afni.
> the "latest afni version" on the first webpage
> says AFNI_2011_12_21_1014.
> The afni -ver on my macbookpro say also
> AFNI_2011_12_21_1014.
> Do I have the most recent afni?
There are many versions of afni that all have the same 'Vers
by
nick
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AFNI Message Board
wdo Wrote:
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> Hey, I tried to use 3dttest, however I am getting
> odd results. If I run the exact same script with
> 3dttest++, the outputted BRIK gives me mean values
> that are correct (compared against 3dTstat -mean
> output), and T values which make sense. However,
> the exact same script using 3dttest with -base1
by
nick
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AFNI Message Board
Dear AFNI experts,
I'm playing with the ToyTalk matlab code example to get NIML communication between SUMA and matlab working. More precisely I would like to write my own interactive visualization functions in matlab, that change when the user selects another node on a surface in SUMA.
This seems to work fine, but I have a question about the contents of the communication that SUMA sen
by
nick
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AFNI Message Board
PeterKohler Wrote:
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> Nick, I would love to hear about your
> implementation of whole-brain correction.
I wrote an *experimental* and *not properly validated* (i.e., use at your own risk) python script for this.
it should work with volumes and surfaces.
by
nick
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AFNI Message Board
kblacker Wrote:
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> Second, I know that in volumetric data you use
> 3dClustSim. I did run 3dClustSim to get the number
> of voxels I would need for a given, corrected
> p-value, but I don’t know how to translate that
> into the Area and Conn variables in SUMA. Is the
> 3dClustSim step necessary with surface-based
>
by
nick
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AFNI Message Board
jaredmr Wrote:
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> I have
> 5 runs, each consisting of study block, a test
> block, a baseline block, a study block, and a test
> block, always in that order and each having a
> total of 199 dynamics.
You use a polort of 6, that seems too high. Chances are that you're removing a lot of signal of interest if there a
by
nick
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AFNI Message Board
Linda Wrote:
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> But for the subject.niml.dset, I can not know
> which column contain the value I need. [...]
> The followed is the information I get from the
> SurfDsetInfo and 3dinfo.
> SurfDsetInfo
> v2s.MaskS_unsmooth_corr_movie_gb_11.nii.gz.lh.TS.n
> iml.dset
> [...]
> Data Element:
> dnel->vec
by
nick
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AFNI Message Board
Linda Wrote:
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> I can not open the subject.niml.dset. [...]
> I want to make sure if it is right as followed: [...]
> 3dcalc -a Subject1.niml.dset[6] \
> > -b Subject2.niml.dset[6] \
You would probably want to surround sub brick selectors by single quotes, otherwise the shell interprets them as something special.
F
by
nick
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AFNI Message Board
qiuhai Wrote:
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> Could anyone help to post me a sample of .sumarc
> file. The link on help-file page seems broken.
The default configuration may be a good starting point:
by
nick
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AFNI Message Board
heiding66 Wrote:
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> In our case it would be data-driven using
> 3dExtrema to define the maxima and then define
> clusters around these. How would one break up or
> define the unique clusters around these maxima?
You could use 3dmaskdump or 3dmaskave with the '-...ball' option to get spherical ROIs, for example. N
by
nick
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AFNI Message Board
Linda Wrote:
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> I want to do the group analysis of functional
> data. I have the High-Res.Anatomical(SurfVol) and
> the surface frome freesurfer for each subject. And
> also I get the experiment's
> high-Res.Anatomical(ExpVol) along with the
> functional data.
> I do not know if I should do align the surface
by
nick
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AFNI Message Board
heiding66 Wrote:
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> I still
> don't know how to use 3dExtrema to 'break up' a
> huge cluster into smaller ones to make small
> cluster masks. I just don't know because 3dExtrema
> gives only the single voxels with the maxima of
> the small clusters--just would like to know how to
> apply this i
by
nick
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AFNI Message Board
yfh2013 Wrote:
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> I check the All_lh_ld141.spec in the demo. It is
> as followed:
> #define the group
> Group = All_lh_ld141
>
> #define various States
> StateDef = mappedSphere.reg
> StateDef = mappedSphrNoReg
> [...]
> NewSurface
> SurfaceFormat = ASCII
> SurfaceType = GIFTI
>
by
nick
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AFNI Message Board
heiding66 Wrote:
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> Hello experts!
> I wish to segment a huge cluster which contains
> many "small" clusters of interest.
3dExtrema?
by
nick
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AFNI Message Board
Linda Wrote:
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> My Afni version is linux_gcc33_64.
That's not really afni's version - but actually afni's version system is kinda weird anyway. On two different systems I get
$ afni -version
Version AFNI_2011_12_21_1014
[]
and an older one
afni -version
Version AFNI_2011_12_21_1014
[]
in other words th
by
nick
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AFNI Message Board
yfh2013 Wrote:
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> I want to know the different between the new
> @SUMA_Make_Spec_FS and the old version one. Ziad
> recommend me to use the -GIFTI for
> @SUMA_Make_Spec_FS. But I am not sure if it will
> bring me a lot of trouble , because I am not sure
> the different between the old one and the new one.
This que
by
nick
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AFNI Message Board
Linda Wrote:
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> For the first question, the -GIFTI option is not
> available for the new @SUMA_Make_Spec_FS.
Did you update to the latest version of AFNI?
For me, running
@SUMA_Make_Spec_FS -help | grep "\-GIFTI"
gives
-GIFTI :and surfaces are in alignment with the original
What does it return in yo
by
nick
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AFNI Message Board