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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
Results 4081 - 4110 of 4524
Hi Pengmin,
We now have a Fedora 17 system (I think), so maybe we can look
at this tomorrow. But the error is for libpng12 for the 64-bit binaries.
You do not have libpng12 under lib64, but libpng15. It is strange
that they are named not to be backward compatible. Maybe if it is
good enough, a link would work.
Anyway, we will see...
- rick
by
rick reynolds
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AFNI Message Board
Hi Colm,
If your subjects are not adults, they may be more prone to
motion, making 0.2 perhaps too strict.
Bandpassing uses basically the fraction of frequencies up
to Nyquist as the fraction of DOF that are lost from the
operation (starting with the number of TRs).
For example, assume everything over 0.1 hz is removed in
the BP operation. Then if the TR is 2s (so Nyquist is 1/4
by
rick reynolds
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AFNI Message Board
Hi Colm,
I think those are the main 2 points. Note that we have seen cases where
censoring and bandpassing are done linearly which would fail when done
together (because of too much censoring). It begs the question of exactly
what is left in the data when more parameters have been removed than TRs
exist...
- rick
by
rick reynolds
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AFNI Message Board
Hi Evangelou,
That option has been added. Binaries are compiling right
now, and should be available by this evening, depending
on your system.
Please let me know if you have any questions.
- rick
by
rick reynolds
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AFNI Message Board
Hi Elrond,
We have not actually compiled those binaries in 4.5 years.
The last package is under:
afni/pub/dist/tgz/old_binaries/cygwin.tgz
It is much more recommended to use a native linux system
for analysis. If you are just trying things out, then consider
a virtual system like Oracle's free Virtual Box. If you install
that, then we have a setup available here:
AFN
by
rick reynolds
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AFNI Message Board
Hi Kristina,
The program was not counting available positions for insert
well, so for such a borderline randomization case as yours,
some of the random cases worked, but most did not.
I have fixed that aspect, and the changes should be available
after tonight's build. Thanks for letting me know!
- rick
by
rick reynolds
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AFNI Message Board
Hi Becky,
The error "-wsVars: Command not found." means that the previous
line (ending in -jobs 4 \ ) does not have proper line continuation, i.e.
there are spaces or tabs after the '\'.
So 3dMVM did not see any options after -jobs 4.
- rick
by
rick reynolds
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AFNI Message Board
Thanks for the update, I'm glad things are working.
Based on your updated description of the problem in the PM,
I think there may have been a bug in the AFNI version you
had that was fixed (probably quickly).
- rick
by
rick reynolds
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AFNI Message Board
Hi Tom,
What does "nifti_tool -disp_hdr" say about the .nii file?
I would be interested in seeing the output starting from
the sform/qform_codes.
Maybe those transformations are different.
- rick
by
rick reynolds
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AFNI Message Board
Hi Gaurav,
I am not seen anything strange here. Certainly old blobs could
disappear at a given threshold. Having new blobs appear suggests
that the threshold is at a higher q-value than the original threshold
t-stat would translate to.
Note that this is not a 1-1 mapping. If the t-stats get smaller, it
does not imply that the q-stats will, that depends on the data.
If you really t
by
rick reynolds
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AFNI Message Board
Hi Isaac,
This should be fixed now, and will be available the next time
binaries are compiled.
Thanks for bringing it up!
- rick
by
rick reynolds
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AFNI Message Board
Hi Srihasam,
I suspect you have a slice that is all zero at time 95
or 96, which the program does not like. Would you
check that?
- rick
by
rick reynolds
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AFNI Message Board
Years ago, I would not have expected it, but mid-command
comments work in current tcsh scripts, though maybe some
would not support it. 'Command not found' was not mentioned.
- rick
by
rick reynolds
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AFNI Message Board
Hi Becky,
Those other python files shoud be in the same directory.
Perhaps you do not have the entire set of binaries (in that
directory). Is afni_proc.py there, for example?
- rick
by
rick reynolds
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AFNI Message Board
Indeed, it isto good to censor anything that looks bad,
Though automatic censoring is preferred. Note that
outlier censoring probably does a better job than motion
parameter censoring, so doing both is a nice way to go.
See -censor_outliers in the afni_proc.py help.
- rick
by
rick reynolds
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AFNI Message Board
Hi Guillaume,
Those numbers do not sound too bad to me.
Hitting 10% does seem like a lot, but more
important is the fraction of each stim class that
is lost.
Look at the final output from the afni_proc.py
script (or re-run the @ss_review_basic script).
Choose a fractional limit of response TRs lost
for any stim class to drop a subject, as well as
an overall fractional limit. Ma
by
rick reynolds
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AFNI Message Board
Hi Kristina,
What is the contents of the last out.mrt file?
That should contain any error messages.
- rick
by
rick reynolds
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AFNI Message Board
Hi Jessica,
If you really want to have each grouping of 4 have exactly 1
stop stimulus, then this seems reasonable. But as there are
still only 2 stimulus classes, there should only be 2 stim files
given to 3dDeconvolve (or afni_proc.py).
You can use timing_tool.py to put the 4 stop files together,
and then the 12 go files. Input one stop file, and then use
multiple -extend option
by
rick reynolds
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AFNI Message Board
Hi Nicole,
You can load those datasets in suma just like any other
stats dataset, but the special addition is to use the 'g' key
to plot the graph at any given node.
- rick
by
rick reynolds
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AFNI Message Board
Hi Dante,
We no longer have computers of those types that we
compile on, and the binaries have not been compiled
since March.
Consider this thread:
afni.nimh.nih.gov
- rick
by
rick reynolds
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AFNI Message Board
I don't have much to add beyond Isaac's response, except to
note that afni_proc.py will censor based on outliers if you use
the -censor_outliers options.
- rick
by
rick reynolds
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AFNI Message Board
I expect that if fink is distributing openmotif, then there
is probably no licensing issue with it on mac. Note that there
was a period of time when it was not being included. Yes, it
should matter that Darwin is open source.
There is no reference to /usr/bin/gcc in the 10.7 Makefile that
I see, even throughout the history. Where are you seeing it?
- rick
by
rick reynolds
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AFNI Message Board
Any plotting programs should link the openmotif library.
But the hope is that libmri.a does not. That is to say one
should be able to compile the non-GUI programs without it.
I have not tried that in a long time.
- rick
by
rick reynolds
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AFNI Message Board
Hmmm, where are you looking? It seems current.
You can see all files here:
http://afni.nimh.nih.gov/pub/dist/tgz
Or you can run:
@update.afni.binaries -package linux_xorg7_64
from the command line.
- rick
by
rick reynolds
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AFNI Message Board
Note that "3dresample -rmode NN" might be easier
to use than 3dfractionize.
- rick
by
rick reynolds
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AFNI Message Board
Hi Isaac,
That's odd, we were building libmri.a without any X/Motif
dependencies at all. If it has crept back in, that is unfortunate.
If I have time, I will take a closer look tomorrow.
- rick
by
rick reynolds
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AFNI Message Board
When running 3dvolreg, afni_proc.py uses the -1Dfile
option, rather than just -dfile. The resulting file does not
have the index column or the rms columns.
You should be able to input columns [1..6] to the 1d_tool.py
command.
The units are in mm, though that is approximate, since
three of the parameters are in degrees. But a one degree
rotation is close to 1 mm on the surface of a b
by
rick reynolds
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AFNI Message Board
Hi Noah,
To use motion as a covariate, you want just 1 number per
subject, not 6 times 1000 numbers.
Collapse the 6 motion columns down to a single a single
average motion estimate using 1d_tool.py and 3dTstat. See
this current thread for details and an example:
afni.nimh.nih.gov
- rick
by
rick reynolds
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AFNI Message Board
It is a really good idea to at least test and compare with
the afni_proc.py stream, but that is a different topic...
Try these 2 commands (assuming 3 equal length runs):
1d_tool.py -infile motion.1D -set_nruns 3 -derivative -collapse_cols euclidean_norm -write enorm.1D
3dTstat -prefix - enorm.1D\'
- rick
by
rick reynolds
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AFNI Message Board
Hi Kym,
Yes, afni_proc.py outputs that by default at the end of the
processing, both for censored and uncensored motion, by
running the 'basic' script output by gen_ss_review_scripts.py.
Check "average censored motion" from out.ss_review.*.txt,
for example.
- rick
by
rick reynolds
-
AFNI Message Board