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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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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 4411 - 4440 of 4524
Hi John,
Glad to hear you got it working. I keep forgetting about the gcc version option
(there is a problem in the gcc compiler with the natural version on our build
machine).
To add a library to one program, you can add it on the compile line for that
target, e.g. the compile line after the one starting with "3dRegAna:" in
Makefile.INCLUDE. But it's okay to add it
by
rick reynolds
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AFNI Message Board
Hi Vanessa,
If you are not already using afni_proc.py to analyze your data,
consider how it suggests to run a script:
if using tcsh: tcsh -xef SCRIPT |& tee output.SCRIPT
if using bash: tcsh -xef SCRIPT 2>&1 | tee output.SCRIPT
For details, please see the section "SCRIPT EXECUTION NOTE"
in the help output:
afni_proc.py -help
- rick
by
rick reynolds
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AFNI Message Board
Ick. That bit from the afni_proc.py help is a mistake, and I
will fix it.
The "FATAL ERROR: ... no aux values" message is coming from
3dDeconvolve, and the only fix is to do what it says. For the
case of married times, do not use '*' but -1:0, for example.
Thanks for bringing up the AP help,
- rick
by
rick reynolds
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AFNI Message Board
The main question for the group analysis is whether you are going
to use an AUC (area under the curve) approach, or to look for group
differences in the shape of the curve. AUC is much easier, of course.
- rick
by
rick reynolds
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AFNI Message Board
If the anatomical contrast shows the boundary that you want to use,
the 3dSeg might help. But one question might be how to define the
boundary in the inferior direction. That seems murky.
Also, I think there can be much more than just CSF between the brain
and the skull.
Maybe we should ask Ziad (the author of 3dSeg) to suggest how to
use it that way. But even the default usage shoul
by
rick reynolds
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AFNI Message Board
To all posters on this message board,
Getting an account and logging in will allow you to control
the view of topics (threaded, etc.) and will allow sending of
private messages to or from us.
The benefits are not huge, but might certainly make using
the board more pleasant for you.
- rick
by
rick reynolds
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AFNI Message Board
Hi Gaurav,
It is fine to run t-tests on normalized R values (via the Fisher Transform, say).
For instance, if you were using InstaCorr on some subject, as you drag the
mouse around it would compute changing correlation maps for that subject.
Using GroupInstaCorr would work the same way, except that after computing
each subject's R map, it would normalize (via Fisher) the maps, then d
by
rick reynolds
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AFNI Message Board
Hi Kyle,
The person you may need to communicate with is Gang, who will not
be back for a while (though he might occasionally check the board).
Please be patient.
TENT functions are much more difficult to deal with at the group
level, because you are not just dealing with a single beta (unless
you want to take some area under the curve approach). So that means
you should try reading so
by
rick reynolds
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AFNI Message Board
Hi Liesel,
First, let me be sure what you mean (the "NOT brain volume" does not
quite clarify it to me).
Do you mean everything within the skull? If so, computing the volume
of an anatomical mask might be reasonable. However those are not meant
to be precise. To be precise might mean measuring the volume contained
within the pial surface.
Do you mean only Grey matter? I
by
rick reynolds
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AFNI Message Board
Hi John,
Since you are running a current 64-bit Linux OS, the linux_openmp_64
package and Makefile should be the most appropriate.
However our Makefiles are set up for our convenience in distribution,
not for building on fresh machines. Consider some changes to the Makefile:
- change LGIFTI to -lexpat (to use a shared library)
- comment out USE_LOCAL_X_TREE
- uncomment XLIBS = -lXm
by
rick reynolds
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AFNI Message Board
Hmmmm, I don't see an easy way to do that. There is an -nzmean option,
akin to that of 3dMean.
If we did not have to worry about taking the average of value in the even
case, I could see doing it in a few commands using 3dTsort, 3dTstat and
3dcalc. But that is ugly in any case.
...
Okay, so I added an -nzmedian option to 3dTstat. Do you need that tonight,
or can you wait for
by
rick reynolds
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AFNI Message Board
I wondered about that. There is an -scr_overwrite option to overwrite
the created processing script.
In general, we try to avoid deleting files.
Glad everything worked out!
- rick
by
rick reynolds
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AFNI Message Board
If you are using dmBLOCK for duration modulation, then
it is likely that you want stim type AM1 (less likely is AM2).
IM is to get a different beta for each stimulus event, which
is probably not what you want. In any case, IM does not
accept married parameters.
- rick
by
rick reynolds
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AFNI Message Board
Hi Kyle,
That is a fine way to view the IRFs. You can threshold on any
statistic that you want, but of course there is little use in the
individual TENT stats. A composite F might be more useful.
The individual TENT betas are not great for overlay either. If
your goal is just to peruse single subject results, maybe look
at the IRFs as you are, with both OLay and Thr as the same
comp
by
rick reynolds
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AFNI Message Board
Hi Kyle,
You can use the exact same time_times file for BLOCK() or TENT(), say,
a single run of local times for each run, as you said.
On the flip side, result of using TENT will be columns of the regression
matrix that are 1s and 0s (or fractions, for non-TR-locked stimuli and TENTs).
But you don't generate this, 3dDeconvolve does.
- rick
by
rick reynolds
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AFNI Message Board
There should be no reason why you cannot use -giant_move. That means
there is surely just some mistake that we want to figure out.
I'm a little confused. Reviewing your previous post, it looks like
you are specifying -giant_move in the command, but it is not shown
in the command from the bottom of the script. That would be really
strange.
By the way, you seem to have --regress_s
by
rick reynolds
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AFNI Message Board
That is right. That is why it refers to -surf_anat as a "missing dataset".
The surface options were added in October, 2011.
- rick
by
rick reynolds
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AFNI Message Board
Hi Ana,
I do not think make_random_timing.py can currently do that.
Would the jitter between blocks differ from that between events?
- rick
by
rick reynolds
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AFNI Message Board
Hi ASI,
The processing script that was generated by afni_proc.py has the
regression step in it (using 3dDeconvolve). I suggest you make a
copy of the script and remove everything but that 3dDeconvolve
command, and then change it to suit your needs.
- rick
by
rick reynolds
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AFNI Message Board
Hi ASI,
There seem to be 2 mistakes with your command.
One thing that sticks out is -epi2anat (applied via -align_opts_aea).
That option is not appropriate when using afni_proc.py (the decision
needs to go through afni_proc.py so that it knows).
You have specified to align the EPI to the anat in afni_proc.py via
-volreg_align_e2a. Do not include -epi2anat in the AEA options.
Also,
by
rick reynolds
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AFNI Message Board
Let me reiterate the suggestion of sending email directly
to the author, as shown on the bottom of the help output.
Please provide him details such as your experiment design
and the format of your datasets.
- rick
by
rick reynolds
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AFNI Message Board
Hi David,
While 3dTstat has a median option, it only takes one input. You could
create that input as a dataset using 3dbucket:
3dbucket -prefix stats.all stats.subj*+tlrc.HEAD
or you could specify the inputs directly to 3dTstat, within quotes, so
they would be read as one catenated dataset anyway. Note that since
wildcards won't expand within quotes, we cheat with the backward
by
rick reynolds
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AFNI Message Board
Hi Sandra,
Note that afni_restproc.py was written by Rayus Kuplicki of Tulsa.
If he does not notice your posting, contact him via the information
at the bottom of the help output.
We process resting state data using afni_proc.py and/or @ANATICOR.
- rick
by
rick reynolds
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AFNI Message Board
No, the output will simply be the subtraction A-B at each voxel,
along with any statistics you have asked for. With that GLT you
are asking, "where is the contrast A-B different from 0"? The
betas for A and B are already in the output dataset.
- rick
by
rick reynolds
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AFNI Message Board
Start by reading the output of "3dsvm -help". The end of the help mentions
contact information for the author, Stephen LaConte.
For more details on the afni GUI, click on "AFNI Tips" along the bottom of
the main controller.
- rick
by
rick reynolds
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AFNI Message Board
Hi Pat,
I would be inclined to use the same basis function as with the
classes of interest, and in any case, use -stim_times.
Of course it really depends on the task, and in what way the
subjects are failing to perform.
- rick
by
rick reynolds
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AFNI Message Board
1. Even if you don't do the regression with afni_proc.py, you can still
generate a complete proc script just to see what it does.
2. There is a new -regress_stim_types option that lets you specify the
timing types, including times, AM1, AM2 and IM.
3. As Peter mentioned it is really easy to create a complete processing
script and then just change -stim_times to -stim_times_
by
rick reynolds
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AFNI Message Board
The only reason it is done is to make the constant polort terms
more like the average baseline per run, which some people use
for computing percent signal change. If you are not using those
constant polort terms, then it does not matter which motion terms
you use.
Heck, if the motion terms are given along with -stim_base (such
as with afni_proc.py) then it completely does not matter.
by
rick reynolds
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AFNI Message Board
Yes. I cheated and made a link from /usr/include/openmotif/Xm to
/usr/include/Xm (since I did not want openmotif to be special).
Note that lesstif is not a reliable replacement for openmotif.
I think the xorg-x11-fonts-misc package provides the fonts used in afni.
- rick
by
rick reynolds
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AFNI Message Board
Hi SJ,
Demeaning the motion parameters should only affect the constant
polort betas. The betas for regressors of interest should be unchanged.
- rick
by
rick reynolds
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AFNI Message Board