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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
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I am having the same problem. I ran the test command and got this. It does look like there are some problems... but I don't know how to fix.
kefka:/Volumes/lt-tib/mbsr-working/scripts$ afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 14.5.0
versi
by
dperlman
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AFNI Message Board
For what it's worth, here's exactly what I had to do to get 3dSkullStrip to work, after downloading the most current precompiled binaries:
sudo install_name_tool -change /sw/lib/libiconv.2.dylib /Applications/afni/libiconv.2.dylib 3dSkullStrip
sudo install_name_tool -change /sw/lib/libglib-2.0.0.dylib /Applications/afni/libglib-2.0.0.dylib 3dSkullStrip
sudo install_name_tool -chang
by
dperlman
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AFNI Message Board
The docs I read about 3danisosmooth make it seem like in theory it should be able to do what I need, but it's not clear if it's actually possible.
Basically I have an anatomical T1-weighted brain image from some fancy new motion-resistant pulse sequence (we were scanning kids). For whatever reason, this image type has ended up with the layer of CSF between the brain and skull showing
by
dperlman
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AFNI Message Board
Thanks for letting me know about 3dQwarp, I didn't know about that yet. It looks like that would have been great if we had had that back a few years ago when this data set preprocessing stream was agreed upon by a (inconveniently large) group of researchers. But we're stuck with what we have now.
Also, the example in the documentation for 3dQwarp has epis being warped and resampled
by
dperlman
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AFNI Message Board
So to clarify, the individual subject coefficient maps were transformed to 2mm^3 resolution when they were transformed to MNI atlas space with SPM's DARTEL. This is a decision that is bigger than me and I can't change it, not that I would if I could. So what I'm asking is not whether I should change the resolution; I'm asking how to properly run monte carlo simulation given
by
dperlman
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AFNI Message Board
Something I've been wondering about for years: every explanation of AlphaSim or 3dClustSim talks about the tradeoff between p-value and cluster size in very vague terms. For example Gang Chen's web site says "Basically you need to compromise among overall significance level (alpha), minimum cluster size, and individual voxel significance level, and may have to vary different p val
by
dperlman
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AFNI Message Board
Wow, major bonus. I use bash and I know a lot of bash tricks but this hammer is new to me. Thanks!
Also just for the record, not every program interprets - to mean "read from standard input". That's not a bash thing, that's something that some programs have decided to do on their own. I know you know that Isaac, just wanted to put it in this thread for anyone else learn
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dperlman
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AFNI Message Board
Is there an afni way to add up, say, columns 27 through 46 of a 1D file?
I could do it with something like -a 27 -b 28 etc. but seems like I'd run out of numbers.
I was wondering if there was something that would take an argument like 1drowsum file.1D[27..46]
I tried this but it didn't work, none of these guys seem to be able to read from stdin:
1dtranspose glm_byT_ir2TR_ant
by
dperlman
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AFNI Message Board