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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:
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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
Results 4441 - 4470 of 4524
Hi Becky,
That makes me wonder about the alignment. If you run afni and suma together
to view the surfaces on the anatomy in the .results directory, do they look aligned?
Also, does the EPI look well aligned with the anatomy?
- rick
by
rick reynolds
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AFNI Message Board
Hi Anthony,
You should be able to use the same commands that would apply to the volume,
but with the 1D or .niml.dset or .gii.dset datasets.
So the answer to both questions is yes, though processing with large 1D datasets
is faaaaar slower than using datasets in .niml format.
- rick
by
rick reynolds
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AFNI Message Board
I finally got to try this on 2 10.7 systems (one with XCode and fink,
and one with neither), and there were no problems on either system.
So that begs the question of whether you had some problem either
downloading or extracting that program.
Maybe you should just update your binaries and try again. Or just
download that one program and see how it goes.
- rick
by
rick reynolds
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AFNI Message Board
Hi Becky,
One difference may come from the smoothing level. The default with
volume analysis is to apply the blur_size as an addition smoothing via
3dmerge. But in surface analysis, it is applies as blurring TO that size.
So you might consider going with a higher blur_size in a surface analysis.
Other than that, there should be little difference.
- rick
by
rick reynolds
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AFNI Message Board
So you are piecing things together to be able to run that?
For comparison, you might try afni_proc.py.
In any case, your .HEAD and .BRIK files should have a view,
such as stats.AA090911+tlrc.HEAD.
But gen_ss_review_scripts.py actually figures some things
out from the dataset headers, and so renaming might not be
good enough.
Note that you can specify datasets on the command line, a
by
rick reynolds
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AFNI Message Board
Hi James,
libtracktools.a seems to be compiled under afni_src, so there must have
been a compile error farther up for that.
Make it directly and note the errors from that: make libtracktool.a
-rick
by
rick reynolds
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AFNI Message Board
Hi Gabe,
No, I just messed up what I wrote. Hopefully it was clear that 6.07
was the voxel diagonal, and not the volume.
Thanks a lot for pointing it out!
- rick
by
rick reynolds
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AFNI Message Board
I'm not quite sure what to say about this.
Do you have openmotif on your computer? Would it be possible
for you to compile your own binaries?
- rick
by
rick reynolds
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AFNI Message Board
You mean versions 12 and 15, right? If your newer version of
libpng is not backward compatible, that is a problem.
What is the output of this?
ls -l /usr/lib*/libpng*.so
- rick
by
rick reynolds
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AFNI Message Board
Hi Kylin,
The last 10.5_Intel package that was compiled was on May 2. It seems
that we have stopped building that package, though I do not know why.
If you want the May 2 package, it is under:
http://afni.nimh.nih.gov/pub/dist/tgz/old_binaries/macosx_10.5_Intel.tgz
- rick
by
rick reynolds
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AFNI Message Board
Hi Angel,
To be sure, you mean that alignment with align_epi_anat.py succeeded
before the current correction, but it failed afterwards, is that right?
When you look at the corrected and uncorrected images in afni, are they
in the same place? Are they on top of each other. While the -diff_hdr
output shows a different orientation matrix, that alone does not say
enough.
Also, were the
by
rick reynolds
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AFNI Message Board
Hi James,
The Makefiles are set up for us to distribute binaries easily,
not for easy compile of a new machine. In the cases where we
specify a path to a static library, you probably want to use a
dynamic linking, instead. That applies to libXm, libXt, libexpat,
at least.
Also, the gcc33_64 Makefile is not the best place to start. As
your system is new, go with openmp_64 (so that yo
by
rick reynolds
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AFNI Message Board
It might clarify things to see you command and to know what you plan
to do after this step. A conversion might not even be needed.
But anyway, 1dcat should work on a 3D dataset.
- rick
by
rick reynolds
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AFNI Message Board
How about this version?
http://afni.nimh.nih.gov/sscc/staff/rickr/pub/afni.linux_glibc22
- rick
by
rick reynolds
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AFNI Message Board
Hi Nobuko,
I am doing a build that includes a change to allow (but still
whine about) the num_dim violations that mris_convert has
introduced.
Your linux_xorg7_64 package should be ready in a couple of
hours. Check that the timestamp is from today.
Or just do an update in the morning.
Please let me know how it goes.
- rick
by
rick reynolds
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AFNI Message Board
Hi Guillaume,
That might just mean that you have another instance of afni running
using plugouts. So that port is occupied by the other program.
Or maybe you are on a multi-user system and someone else is
doing it.
@AddEdge might not have been updated to use the -nbp options
for specifying base ports.
I am not sure about the different colored lines. Someone else will
have to chime
by
rick reynolds
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AFNI Message Board
Hi Nobuko,
So these surface datasets were created by FreeSurfer?
They are not in a valid GIfTI format.
Would you upload some of those '*.gii' surface files? I
can look at working around this.
Also, you should tell the FreeSurfer people about this.
- rick
by
rick reynolds
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AFNI Message Board
That sounds strange. There does not seem to be a problem
when using the current set of binaries (June 12).
It's possible something was changed and fixed, though I did
not hear about it. Try a local copy of the current version:
http://afni.nimh.nih.gov/pub/dist/bin/linux_openmp_64/afni
- download
- make executable: chmod 755 afni
- try it: ./afni
Thanks,
- rick
by
rick reynolds
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AFNI Message Board
Note that a right-click is not intended to move the crosshairs,
if that is what you are expecting. The bg value will not update
unless the crosshairs are moved (with a left-click).
Since the right-click is for a menu of actions, it would not be
appropriate to move the position.
- rick
by
rick reynolds
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AFNI Message Board
Those are not bash scripts, but tcsh.
Either run them by using ./ (which is done at the end
of your single subject proc script), or by using tcsh:
a) ./@ss_review_basic
b) tcsh @ss_review_basic
- rick
by
rick reynolds
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AFNI Message Board
Hi Mingbo,
Do you happen to have 32-bit libraries on that machine?
Might the linux_glibc22.tgz work for you?
Try http://afni.nimh.nih.gov/pub/dist/bin/linux_glibc22/afni
for an initial test.
- rick
by
rick reynolds
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AFNI Message Board
Hi Nick,
Many people will still be in Beijing next week, including Ziad.
So please be patient, and maybe bump this up yourself after
the 25th.
- rick
by
rick reynolds
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AFNI Message Board
I am still waiting to try this on 10.7. I hope that in the meanwhile,
you are using 3dDeconvolve. Note that we generally do not use
3dfim+.
Hopefully today, and sorry for being slow...
- rick
by
rick reynolds
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AFNI Message Board
Hi Chris,
Is this via a remote connection? Do other X11 programs work, such as afni?
- rick
by
rick reynolds
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AFNI Message Board
Hi Nobuko,
I must wonder whether you have write permissions in the directory you are working.
Just to be sure...
Otherwise, Ziad will have a difficult time answering while they are in Beijing teaching.
So would you run the same command, only using "tcsh -x", and mail me the output
(do not need to post it on the board)?
For example, assuming SUMA_MS_FS is in your abin, run
by
rick reynolds
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AFNI Message Board
I wondered about that from your link. But it seems like a great
idea in any case!
- rick
by
rick reynolds
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AFNI Message Board
If the mouse is slow, I wonder whether you have enough RAM to run
both the windows OS and linux with AFNI programs.
In any case, I suggest you read some documentation, at least starting
with the AFNI GUI. Here are our class handouts:
http://afni.nimh.nih.gov/pub/dist/edu/latest/afni_handouts
At least look over the GUI slides (afni03_interactive.pdf). You might want
to get your f
by
rick reynolds
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AFNI Message Board
Your version of that program is not current, so I would expect that it
is no longer a problem. Are you able to update your binaries?
@update.afni.binaries -defaults
- rick
by
rick reynolds
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AFNI Message Board
Hi Mingbo,
Your interpretation is correct, it should be like 3dBlurInMask.
- rick
by
rick reynolds
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AFNI Message Board