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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
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I would like to get a mesh outline for my volumetric data, preferably in .ply format. I have found that AFNI's ConvexHull executable does pretty much what I need, except, of course, that the shape is convex. I am working with mouse brains, which have quite a bit of concavity (though a lot less than the human brain).
Any idea how I can get a nice mesh model from my NIfTI templates?
by
TheChymera
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AFNI Message Board
Since 3dBlurToFWHM uses the temporal noise profile to estimate the smoothness - does it make a difference whether I use it before or after the bandpass? I tried to empirically determine this by measuring the smoothness before and after bandpass with 3dFWHMx, and it seems my bandpass increases the smoothness just a bit.
So I suppose it does.
Would you recommend I smooth before or after the b
by
TheChymera
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AFNI Message Board
Can I use `3dmerge` to do an anisotropic blur (similarly to `3dBlurToFWHM`)?
As I understand it, `3dBlurToFWHM` does some blur monitoring which allows it to more accurately smooth anisotropic data. I'm wondering whether this is also the case for `3dmerge`.
by
TheChymera
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AFNI Message Board
Hello guys, many thanks for doing this!
I am working on packaging AFNI for Gentoo, and am experiencing much of the same frustrations you referred to with the current multi-makefile-based build system.
I would be very interested in using your sources for the Gentoo build, but sadly, I found the NeuroDebian infrastructure rather intransparent, and could not locate the sources (also, the link
by
TheChymera
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AFNI Message Board
Hello, I have been working on packaging AFNI for Gentoo Linux for a while now, and, while the current ebuild (Gentoo package atom) works, it does so by cutting a lot of corners.
Among many other things, to make AFNI kind-of compile right, I have to hack one of the Makefiles with sed, and delete some of the stuff bundled in AFNI after it has been already compiled. I was thinking of fixing this
by
TheChymera
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AFNI Message Board
Thanks rick,
What is the difference if I install from (as recommended in your instructions) or from github? Is afni_src.tgz just a (nightly?) archive of your repo's /src ?
by
TheChymera
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AFNI Message Board
Man thanks for your reply!
Are you sure that the prog_list.txt file still exists? I was unable to find it:
```
chymera@zenbookhost ~/afni_src $ find . -name prog_list.txt
chymera@zenbookhost ~/afni_src $ find . -name prog_*
./prog_opts.c
chymera@zenbookhost ~/afni_src $ find . -name *_list.txt
```
by
TheChymera
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AFNI Message Board
Hi, I am packaging AFNI for Gentoo following the official compile/install guide ( ).
Instead of /abin I am using /opt/afni, as it seems better suited to Gentoo practices. I am also adding that directory to PATH.
After compilation, naturally, none of the files have run permissions, I could just do this the crazy way and add permissions to everything under /opt/afni - but maybe you could poi
by
TheChymera
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AFNI Message Board
Ok, that worked, now I just have to figure put how to have portage do that at install time and how to even out some ofther things like versioning and pulling from the live link with the gentoo devs. I believe in a week or so AFNI will be in the gentoo-science overlay.
One issue which would really save us a lot of trouble - can't we even get read access to CVS - for pulling the builds?
by
TheChymera
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AFNI Message Board
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.
Cheers
by
TheChymera
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AFNI Message Board
Well yes, I want this build to eventually be usable by any gentoo user, anywhere.
No, I was asking about the atlases and co. Are they freely available? where?
Also, I seem to have a weird problem, I gather afni should be callable on the cli with "afni" - that won't work, and neither do I find any file named afni in the compile dir. These are my files - which one is the la
by
TheChymera
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AFNI Message Board
Yes, I want to publish this to the gentoo-science overlay (which holds ebuilds for scientific software which are not yet solid/used enough to be put in gentoo proper).
What do you mean by what perspective I ask from? by the source distribution you mean what is under ? What should I do to get those?
3) I will not need to add funstuff/ to the path - will I?
by
TheChymera
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AFNI Message Board
Gentoo uses emake - I don't know in how far that is different from cmake. Do you have any debian-specific makefile which I could test on my gentoo builds? who knows, maybe it will work better than the builds which come packaged with afni.
by
TheChymera
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AFNI Message Board
Hello, I have successfully removed the second make install call (to the protests of gentoo maintainers) and added a mv call instead ( ) - now EVERYTHING in the afni build directory gets copied to /opt/afni . The gentoo people told me this (keeping the entire build dir) is a horrible idea. What do you think?
In any case I have a couple of questions pertaining to the package:
1) do you have
by
TheChymera
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AFNI Message Board
I switched to the other makefile and I believe I am getting the same error
Are you sure I need to alter the makefile here
LGIFTI
and here
XLIBS
?
I am thinking the last line in my ebuild ( emake -j1 totality suma XLIBS="-lXm -lXt" LGIFTI=-lexpat ) does just that - or does something in the output lead you to believe that it fails somehow?
by
TheChymera
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AFNI Message Board
Hey, I think I fixed the multithreading thing (changed the default emake settings on ym machine) - but now I get other errors, apparently some files don't get found:
Cheers,
by
TheChymera
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AFNI Message Board
Hm... Ok, I rectified that.
Using this file I get this
Apparently it's already in the eispack directory (see line 6142/6143):
cd eispack/ ; make all 'CC=/usr/bin/gcc -O2 -m64 -fPIC -DREAD_WRITE_64 -DLINUX2 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE -DDONT_USE_XTDESTROY ' 'CCSVD=/usr/bin/gcc -O0 -m64 -fPIC' ; /bin/mv -f *.o .. ;
by
TheChymera
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AFNI Message Board
Many thanks for the input - it seems to have solved the problem, but I am running into another one further down the line. I have this ebuild now and get this output
Best,
by
TheChymera
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AFNI Message Board
oh, sorry, I thought I had also pasted my error output - here you go:
by
TheChymera
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AFNI Message Board
Hello, I am trying to write an ebuild (Gentoo package atom) for AFNI. This would enable Gentoo users to compile the newest AFNI on their systems via a single command. If there is any sort of repository with versioned AFNI releases, the Gentoo package manager would even take care of keeping AFNI up-to-date. In any case, I am having some issues which I believe root in part in missing deps and in pa
by
TheChymera
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AFNI Message Board