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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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Pages: 123
Results 31 - 60 of 71
Daniel,
Hi. This looks very alright to me. Thanks, friend.
Sincerely,
Dante
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dante.picchioni
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AFNI Message Board
Dear Colleagues,
Hi. I have a problem with the "Go to atlas location" AFNI feature. Please correct any statements that are misunderstandings along the way.
At first, I had no environment variables set. I would use
TT_N27_SSW.nii.gz
as my underlay and
TT_N27_EZ_ML+tlrc.*
as my overlay. Fun. Great. If I wanted to use "Go to atlas location," I could use the defaul
by
dante.picchioni
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AFNI Message Board
Daniel,
Hi. How have you been? That does not seem to have the same slides as in the video, specifically Slide 17 with the website resources. I also checked
with the same result.
Sincerely,
Dante
by
dante.picchioni
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AFNI Message Board
Dear Colleagues,
Hi friends. I will soon manually categorize the regions in the "Eickhoff-Zilles macro labels from N27 in Talairach TT_N27 space" (AFNI_atlas_spaces.niml) available with AFNI. I will categorize them into superordinate categories (e.g., default-mode network). I prefer using these regions rather than functionally defined regions because the anatomy has fewer assumpti
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dante.picchioni
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AFNI Message Board
Dear Colleagues,
Hi. When I click on Under- or OverLay, how are the shown datasets sorted?
Sincerely,
Dante
by
dante.picchioni
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AFNI Message Board
Paul,
You're right. Maybe I will use some sort of linear mixed model or select a random subset of voxels in the larger regions to match the smallest region.
Sincerely,
Dante
by
dante.picchioni
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AFNI Message Board
Dear Colleagues,
Hi. I’m having fun with 3dNetCorr. (Of course, it’s very serious science. Serious. Serious. Harrumph, harrumph.) I appreciate its ease-of-use; I was able to get preliminary results very quickly. If I wanted now to get partial correlations with region size partialed out, should I stick with it, or might you recommend another AFNI program?
Sincerely,
Dante
by
dante.picchioni
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AFNI Message Board
Rick,
Hi. Initial testing was successful. Thanks again.
Sincerely,
Dante
by
dante.picchioni
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AFNI Message Board
Rick,
Hi. I will test this soon. Thanks!
Sincerely,
Dante
P.S.: To get a perfect brain, I would need to scan you!
by
dante.picchioni
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AFNI Message Board
Dear Colleagues,
Hi. I am afni_proc.pying data that has already been afni_proc.pyed. Here are the blocks for afni_proc.py #1:
despike tshift align tlrc volreg mask regress
. For afni_proc.py #2, I am trying to apply
blur mask regress
and, during the regression, apply a whole brain anat mask that I have already created. I was open the redundancy of recreating it with
-mask_apply anat
by
dante.picchioni
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AFNI Message Board
Daniel,
Thanks! What is the "virtual Zoom-based AFNI training class" that is mentioned in the first link?
Sincerely,
Dante
by
dante.picchioni
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AFNI Message Board
Dear Colleagues,
Hi. I was born in 1976. My mother and father were both hairdressers in New York City; that's how they met. ... Sorry, let me skip ahead. In the last year or so, I have been refreshing, updating, and solidifying my AFNI skills a little by rereading some AFNI Bootcamp materials and rerunning the associated hands-on exercises. In doing so, I put together a syllabus of
by
dante.picchioni
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AFNI Message Board
Dear Colleagues,
Hi. First, I need to sincerely spread a little more love for AFNI. I really appreciate its ever-improving, up-to-the-minute nature that combines the latest computer science with the latest neuroimaging science. And of course all the detailed documentation and videos and patience with its users!
What is your recommendation about multiple-testing correction at the single-s
by
dante.picchioni
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AFNI Message Board
Paul,
Let's see, for CPUs,
(base) picchionid@raid ~> afni_check_omp
8
, and for the partition, I must assume the default because I did not specify it in my sbatch command,
sbatch -Wv --cpus-per-task=72 slurm_afni.sh
, but I don't know what the default is because it is not listed here:
$ sbatch -help | grep -i -A 10 partition
-p, --partition=partition partition
by
dante.picchioni
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AFNI Message Board
Paul,
Thanks so much for this detailed answer! I appreciate it. Your bottom-line advice is the same that Hendrik Mandelkow gave me, but I wanted to learn a little more from SSCC.
Yes, I accounted for queue time when comparing Jacco de Zwart's raid to NIH's Biowulf. Here are my notes.
RAID:
Sun Jan 3 08:20:12 EST 2021
Sun Jan 3 10:16:51 EST 2021
~2 hr
BIOWULF:
RUN TI
by
dante.picchioni
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AFNI Message Board
Dear Colleagues,
Hi. Let me ask a naive question about using AFNI on Biowulf. I know that things are much more complicated than the way I represent them, but let me oversimplify things so that I can get a rough understanding.
I ran a script that combining
/home/picchionid/afni/CD/AFNI_data6/FT_analysis/Qwarp/s00.warper
and
/home/picchionid/afni/CD/AFNI_data6/FT_analysis/Qwarp/s05.ap.Qw
by
dante.picchioni
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AFNI Message Board
Rick!
Yes! I was able to recreate the graphs from the handouts. Thanks.
Sincerely,
Dante
by
dante.picchioni
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AFNI Message Board
Rick,
Hi again. I actually really like both handouts! afni_TimeSeriesAnalysis.pdf gives helpful didactic details on the experiment, the use of fixed-shape to variable-shape event-related analyses, and the math. afni06_decon.pdf gives a nice hands-on exercise with actual data in a more bite-sized approach and has code that incorporates using afni_proc.py. I for one would love to see one day
by
dante.picchioni
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AFNI Message Board
Rick!
Hi! How are you, sir? Thanks for all your afni_proc.py videos. They were very clear and helpful.
I will take your advice and use the latest handout. And thanks for the data link.
Sincerely,
Dante
by
dante.picchioni
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AFNI Message Board
Dear Colleagues,
Hi. Happy New Year!
On p. 8 of
/home/picchionid/afni/CD/afni_handouts/afni06_decon.pdf
a directory named AFNI_data2 is referenced, but
find /home/picchionid/afni/CD/ -type d -name '*AFNI_data2*'
yields zero results. I also tried to search for some text in the script on p. 9 with
grep -rli 'ToolMovie' ~/afni/CD/
But this also yielded zero results.
by
dante.picchioni
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AFNI Message Board
Paul,
Hi. I worded this question poorly. Let me think about this.
Sincerely,
Dante
by
dante.picchioni
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AFNI Message Board
Dear Colleagues,
Hi. In the context of alignment, are the correlations used in the cost functions what I understand as a "spatial correlation"? That is, are you simply correlating the value at a point in space in the source dataset with the value at the same point in space in the base dataset and then repeating for all points in space? Of course you are not really "repeating;
by
dante.picchioni
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AFNI Message Board
"May your beer be laid under an enchantment of surpassing excellence for seven years!"
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dante.picchioni
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AFNI Message Board
Dear Colleagues,
Hi. I ran the code
CD/AFNI_data6/FT_analysis/s05.ap.uber
associated with A Real Case on p. 11 of
CD/afni_handouts/afni_proc.pdf
and would appreciate some help with understanding the output. Where in
afni_proc.py -help
or elsewhere can I find an explanation of the FT.results output files or generally the contents of the afni_proc.py results directory? I have many quest
by
dante.picchioni
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AFNI Message Board
Dear Colleagues,
Hi. What is the difference between TT_N27+tlrc.HEAD and
TT_N27_SSW.nii.gz? Is it not the case that TT_N27+tlrc.HEAD is already skull stripped and warped?
Sincerely,
Dante
by
dante.picchioni
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AFNI Message Board
Page 2 of 3
Pages: 123