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Dear AFNI users-
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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 4051 - 4080 of 4524
Hi Peter,
Since you currently have timing files in local format, the
easiest thing to do is probably to add surrounding asterisks
for the empty runs. For example, if the current file has one
row of times, but is to become run 5 of 19, then add '*' on 4
rows before the times and '*' on 14 rows after the times.
I do not see any advantage to using global times, and glo
by
rick reynolds
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AFNI Message Board
Hi John,
How did you do the sorting, or were the files already sorted
by volume and then slice location?
It is a little strange that you needed to use 3dresample to
fix the -dicom_org dataset, which suggests there is some
obliquity matrix that is inverted against the -dicom_org
slice ordering. But that suggests that the ordering from
the header is not actually correct, but the alphabe
by
rick reynolds
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AFNI Message Board
Hi Piero,
Yes, 3dresample is appropriate to use. Please provide the
3dsample command that you used and state or show why it
did not work. Then we can suggest how to fix the command.
Expect to use the -master option.
- rick
by
rick reynolds
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AFNI Message Board
Hi Maria,
While I would expect larger voxels to be less sensitive to
small motion effects (but have not studied it), I would still
expect to see spikes due to motion at the levels one
typically censors down to (say 0.2 or 0.3 mm).
In my opinion, the censor level might depend more on
the subjects than on the voxel size. Children and many
other populations will be more prone to motion
by
rick reynolds
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AFNI Message Board
Hi Mahen,
Note that removing baseline and motion is a separate issue
from converting to percent signal change. It is not necessary
to convert to PSC to use 3dSynthesize to remove baseline and
motion.
Do you need PSC for the subsequent analysis?
To convert to PSC, divide by the constant baseline term and
multiply by 100. As mentioned above, what you subtract out is a
different stor
by
rick reynolds
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AFNI Message Board
Thanks again for doing this! I am sorry we have not
gotten to it... :(
- rick
by
rick reynolds
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AFNI Message Board
Hi Maria,
That is good to hear.
Please do not forget to run the _driver script, too! :)
- rick
by
rick reynolds
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AFNI Message Board
Hi Michael,
I believe (less than 100% certain) that you are correct
in that it cannot currently be done. That may sound a
lot like "I don't know", but my certainly is well above
50%... :)
- rick
by
rick reynolds
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AFNI Message Board
Hi John,
Without -dicom_org, the files are taken either in the specific
order they are passed to the program (not typical), or they are
taken alphabetically, according to the input pattern/prefix.
Is sounds like the alphabetical ordering is correct, and using
it Dimon works fine. But there is something odd in a couple of
files that makes the sorting (-dicom_org) fail in the first and
by
rick reynolds
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AFNI Message Board
Then either run the script via:
tcsh @ss_review_basic
or by first doing
chmod +x @ss_review_*
then
./@ss_review_basic
Also, consider running the _driver script.
- rick
by
rick reynolds
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AFNI Message Board
That is very odd. What is the output from the following commands?
ls -l @ss_review_basic
which tcsh
- rick
by
rick reynolds
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AFNI Message Board
Then is the data on an NFS mounted filesystem?
Maybe you losing a fight over network bandwidth...
If that might be the case, when the processing of
some subject seems to stall, see if you can 'cd'
to the data directory.
- rick
by
rick reynolds
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AFNI Message Board
That's a good thought, Peter. They are being executed via
just 'tcsh -c', but I should certainly add a -f in there.
Thanks,
- rick
by
rick reynolds
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AFNI Message Board
Ah. I am not sure what to even do about this.
There are steps during the processing that run tcsh commands
to get output from other programs to use in afni_proc.py (and in
other programs).
In your cases, just starting another t-shell outputs all sorts of
garbage from FreeSurfer, and so that garbage ends up part of,
in this case, the view extension (like +orig).
But it means that afn
by
rick reynolds
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AFNI Message Board
Hi Ben and Nick,
Most of the 3dVol2Surf options are actually part of the vol2surf
plugin for afni. There you can control the mapping live.
- rick
by
rick reynolds
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AFNI Message Board
Hi Krishna and David,
I don't know what FreeSurfer env var might be doing this,
so it is hard to reply to unless I see it. However in the few
cases that I have used FreeSurfer in the past, I would put
those initialization variable in a script and ONLY set them
when I was about to use FreeSurfer.
They set a bunch of variables and manipulate the PATH
(which seems evil to me).
I
by
rick reynolds
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AFNI Message Board
Hi Lu,
If you are using afni_proc.py for the analysis, consider adding
-regress_compute_fitts so that the fitts dataset is created only
AFTER 3dDeconvolve, not by it. That saves maybe 40% RAM.
- rick
by
rick reynolds
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AFNI Message Board
Hi Piero,
Because there was little interest, and it did not seem like a
great idea. Since it has gotten more common in resting state
analysis, I _have_ added bandpass filtering in afni_proc.py.
It is not via 3dBandpass (certainly not 3dFourier), but is done
in the regression itself (3dDeconvolve).
The reason it is part of the regression is so that censoring
could be done properly and
by
rick reynolds
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AFNI Message Board
Hi John,
Thanks for the reminder, too. I was out of the country when
you posted this.
This is a little confusing in that whatever sorting is being
used, it seems to be correct for 77 of the 80 volumes. The
options that you tried look reasonable, though from what you
say the alphabetical ordering of the files matches the proper
slice ordering over time.
Consider adding '-save_
by
rick reynolds
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AFNI Message Board
Oh, sorry. That option is not available in your old binaries...
Yes, unless this is a bad time for it, you should update and
try things again.
Actually, you could convert your mask dataset to shorts and
try again (3dcalc -a T1_mask+orig -expr a -datum short -prefix mask.short).
But it does not really matter if updating is okay for you.
- rick
by
rick reynolds
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AFNI Message Board
Hi Zhan,
It looks like your mask datum is byte, and that the code
does not like it. However I believe that was probably
handled long ago (your binaries are well over a year old).
What is the output of this command?
3dinfo -datum T1.nii T1_mask+orig
You probably just need to update your binaries.
- rick
by
rick reynolds
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AFNI Message Board
Running afni to view the results while the script is
still going should be fine, provided it does not try to
load any partially written datasets.
However it sounds like you may be maxing out your
RAM (including program outside of AFNI - are you
running any MS Office programs, like powerpoint?).
If your RAM is already maxed out, running afni will
just slow things down more.
Try to look
by
rick reynolds
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AFNI Message Board
Is there any chance that you are running out of RAM?
It sounds like 3dAllineate is running at the time. Try
running a 'top' command when it seems to freeze.
More likely there is something else going on.
- rick
by
rick reynolds
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AFNI Message Board
Sorry for being slow on this...
RetroTS is a matlab function written by Ziad to convert those
time series into respiration volume per time signals, as well
as respiration and cardiac phase signals.
See this message board thread for details:
afni.nimh.nih.gov
The AFNI matlab package, of which RetroTS is a part, is here:
afni.nimh.nih.gov
That makes one regressor file per ru
by
rick reynolds
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AFNI Message Board
Hi Peter,
That has been on my todo list for many years now, but
has not happened. What I personally do is just extract
the 3dDeconvolve command from the current proc script
and alter it (with new output prefix names, as well).
That is easy to do, and would be much more work to
modify afni_proc.py. So it has not happened yet. Some
day...
- rick
by
rick reynolds
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AFNI Message Board
Many afni_proc.py options now warn you of a '-' parameter
when it is not expected. The current version would have let
you know.
Glad you found it in any case.
- rick
by
rick reynolds
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AFNI Message Board
Slow drifts due to motion are probably modeled well enough.
Using a slow event related design does not really change
things. If the 2 peak TRs in the middle of a reponse curve
happen to get censored, that does not really matter either
(beyond losing a couple of high variance TRs for the model
estimates).
Also, I do not see any gain in censoring more TRs from that
particular reponse.
by
rick reynolds
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AFNI Message Board
Hi Guillaume,
Slow motion is not such a large concern as far as the signal
goes, unless it gets so big as to affect the shim. Very slow
motion effects are probably reasonably well modeled by the
baseline drifts.
What effect of slow motion drifts are you concerned by?
- rick
by
rick reynolds
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AFNI Message Board
Hi Gaurav,
The main question I have for you is, do you actually
know what the timing is supposed to be? That comes
from the scanning protocol. I have not seen anything
in your posts that suggests what the actual timing was.
Peter had a very nice post about how to apply it, but
you still need to know how the slices were acquired.
Do you know?
- rick
by
rick reynolds
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AFNI Message Board
Hi Pengmin,
I just tried a setup on Fedora 17, and here were the steps.
1. yum install tcsh (and then use as default login shell)
2. wget
3. tcsh @update.afni.binaries -defaults
4. echo 'set path = ( $path ~/abin )' >> .cshrc
5. source .cshrc
6. yum install libXp libpng-compat PyQt4
All you should presumably need is step 6.
Note that libpng-compat installs older
by
rick reynolds
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AFNI Message Board