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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 1 - 30 of 71
Gang,
Hi again. "I assume that you're interested in the cross-brain correlation with the seed ." Yes, I am interested in that.
"Not the scaling factors relative to the response at the ." I am interested in that, also. My ultimate question is: does the response during each arousal correlate with the cross-brain correlations with the seed?
"So, would it be
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dante.picchioni
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AFNI Message Board
Dear Colleagues,
Hi. Can 3dLME accept on-the-fly/runtime-generated datasets? If not, it would be nice if it could.
This code
3dLME \
-prefix output_lme_ranslp_hip_procbasic.nii \
-jobs 8 \
-model 'cond*AAT' \
-qVars AAT \
-ranEff '~1+AAT' \
-SS_type 3 \
-num_glt 1 \
-logLik \
-gltLabel 1 'AATeff' \
-gltCo
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dante.picchioni
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AFNI Message Board
Gang!
Hi, how are you?! I ran 3dLME two times. In reality, I am waiting on the fetal fat_lme_prep.py program to be birthed by Paul for the first one, but let me write in past tense for both.
For the first, I used the Fisher-transformed correlations from 3dNetCorr as input. For the second, I used the unstandardized regression coefficients from afni_proc.py (via 3dDeconvolve) from a single
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dante.picchioni
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AFNI Message Board
Dear Colleagues,
Hi. I would like a voxelwise effect size measure to report alongside (i.e., in a separate map) my eff Z of my within-subject quantitative variable from my 3dLME results. To give a little background, I am determining auditory arousal thresholds about eight times throughout the night during all-night functional MRI sleep studies (https://doi.org/10.1016/j.jneumeth.2018.09.019)
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dante.picchioni
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AFNI Message Board
Paul,
Hi. How are you?
I have made substantial progress on the auditory arousal threshold manuscript that initially spawned this request. The methods, results, figures, tables, and references are about 70% finished (e.g., single seed region results with blurring, effect of physiological preprocessing approach on the single seed region data, etc.). I am now at a point where there is not a
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dante.picchioni
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AFNI Message Board
Gang!
Hi! How are you?! This exchange reminded me to add a citation to your 2013 LME article to the manuscript. It was in my conference presentation, but I was just working on the relevant paragraph in the manuscript!
Hmm. The version for the successful execution was:
[+] Loading R 4.1.3
The version for the failed execution was:
[+] Loading R 4.2.2
Hmm. Should I try using the
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dante.picchioni
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AFNI Message Board
Dear Colleagues,
Hi. I executed identical 3dLME code twice. Once with:
AFNI/current-openmp last updated 2022-05-28
AFNI version=AFNI_22.1.10 (May 20 2022) [64-bit]
and again with:
AFNI/current-openmp last updated 2022-12-26
AFNI version=AFNI_22.3.07 (Dec 2 2022) [64-bit]
No problems with the first execution. With the second execution, I received this error:
Error in if (
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dante.picchioni
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AFNI Message Board
Paul,
Ohhhhh. Thank you for explaining the gestalt of the associated math from the help file. I appreciate your patience. That is awesome: the unique variance explained after removing the variance explained by every other region. Wow. That decreases the limitation that the correlation between region A and B is not direct and is caused by a third region C. I will need to think about that
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dante.picchioni
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AFNI Message Board
Paul,
Hi! At first pass, the CC and FZ matrices look good. Thanks!
The PC matrix is all zeros. However, it is all zeros regardless of whether I use the -wight_corr option. Plus, I assume the input to the fetal fat_lme_prep.py program will be the unstandardized regression coefficients in the PCB matrix, so I assume the PC matrix is not terribly important. Plus, plus, because these are b
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dante.picchioni
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AFNI Message Board
Paul,
Of course, a correlation of something with itself is 1.0. I do not know why I included that detail. I should have just said that all off-diagonal correlations are 0.999 and left it at that.
I replicated your result. When the censor file is all ones, there is no problem. The problem occurs when at least one time point is zero in the censor file. I am almost certain that I am doing
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dante.picchioni
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AFNI Message Board
Paul,
Hi. Okay, now I am shamelessly rebumping because the subject of the post would be identical to this one. Unless you say otherwise, I will assume that you prefer rebumping when the subject is very similar versus starting new threads. Or that you have no preference. The only reason I say that is I very much appreciate help from SSCC and want to make things as easy as possible for it.
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dante.picchioni
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AFNI Message Board
Colleagues,
Hi again. I am sorry. I missed this post that answered my question.
Sincerely,
Dante
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dante.picchioni
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AFNI Message Board
Dear Colleagues,
Hi. Is the -weight_ts option to 3dNetCorr equivalent to the -censor option to 3dDeconvolve? I assume so, but it never hurts to ask. In other words, do time points weighted with zeros have their residuals set to zero rather than using the value of zero in the correlations?
Sincerely,
Dante
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dante.picchioni
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AFNI Message Board
Paul,
Ah, yes. You're right. I forgot that 3dNetCorr wonderfully gives me correlation matrices based on every region of interest's average time series. Thank you for patiently reawakening those circuits in my brain.
Yes, my main result will be the plot generated by 3dLME from the region-to-region correlation matrices that will be fed into 3dLME from 3dNetCorr via the fetal fat_
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dante.picchioni
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AFNI Message Board
Ciao, Paulo!
We must now switch to English, or the conversation would end because I shamefully do not speak Italian. I have to ask you one day where you learned Italian.
Exactly. When I do seed-based functional correlations for one region:
1) I take a region and calculate its mean time series
2) I plop that out to a separate file for later use
3) Only then do I perform spatial smoothin
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dante.picchioni
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AFNI Message Board
Dear Colleagues,
Stop me if you've heard this one. A mechanical, chemical, and software engineer get into a car. It won't start. The mechanical engineer says, "Hmm, we should take apart the starter." The chemical engineer says "What?! No! We should analyze the composition of the battery acid." The software engineer says, "Let's get out and get back in a
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dante.picchioni
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AFNI Message Board
Paul and Daniel,
Success! Thank you, as always, for your patient and intelligent help.
Sincerely,
Dante
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dante.picchioni
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AFNI Message Board
Paul,
Hi. Thank you very much for your help. I hope your trip went well.
I ran the code below. The results are odd to me because the region masks are larger than they should be and have values [0-1].
Sincerely,
Dante
# estimate warp
3dQwarp \
-source /usr/local/apps/afni/current/linux_centos_7_64/MNI152_2009_template_SSW.nii.gz"[0]" \
-base /usr/local/ap
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dante.picchioni
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AFNI Message Board
Paul,
Hi! Thanks for the quick response among the OHBM chaos that I assume you are in the middle of.
Hm. I am probably missing something, but when I visit I am just taken to the AFNI Message Board home page and not to an individual message.
For Way #4, here is the output.
$ afni -VAFNI_COMPRESSOR= >> afni_VAFNI_COMPRESSOR_sto_ste.txt 2>&1
$ cat afni_VAFNI_COMPRESSOR_s
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dante.picchioni
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AFNI Message Board
Colleagues,
Hi. I have read these posts a few times and an appropriate path is still unclear. Any help would be appreciated.
First, let me ask something. Is reviving an old, related post preferred, or would you prefer I start a new post?
I have a similar problem. In my case, I have subcortical-region masks in MNI space (https://www.nmr.mgh.harvard.edu/resources/aan-atlas) and would l
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dante.picchioni
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AFNI Message Board
Paul,
Thanks!!! It's not urgent. Just good to know that it's possible and on one of the burners.
Sincerely,
Dante
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dante.picchioni
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AFNI Message Board
Dear Colleagues,
Hi. Greetings from Charlotte! I used 3dLME for one region's connectivity maps, and it worked great! I presented it yesterday at the annual Sleep meeting, which is a joint meeting of the Sleep Research Society and American Academy of Sleep Medicine.
I took the absolute values of the unstandardized regression coefficients and correlated them with auditory arousal thre
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dante.picchioni
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AFNI Message Board
The Advanced MRI Section (AMRI) in the Intramural Research Program of the National Institute of Neurological Disorders and Stroke at the National Institutes of Health (NIH) in Bethesda, Maryland is seeking a postdoctoral fellow for its all-night EEG-fMRI sleep study.
In addition to developing unique MRI methods for white matter imaging, ultra-low and ultra-high field imaging, and perfusion ima
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dante.picchioni
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AFNI Message Board
Colleagues,
Hi. Does fat_mvm_prep.py have a sibling for use with 3dLME (i.e., fat_lme_prep.py)? I have some data that would fit like a glove onto such a pipeline: repeated behavioral auditory arousal thresholds during all-night fMRI sleep studies. I can guarantee at least homemade Italian amaretti cookies (gluten free, dairy free) to the writer of such a helpful script.
Sincerely,
Dan
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dante.picchioni
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AFNI Message Board
Gang!
Hi! How have you been? Thanks for this.
Sincerely,
Dante
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dante.picchioni
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AFNI Message Board
Dear Colleagues,
Hi. Are there hands-on practice code and dataset available for 3dLME?
Sincerely,
Dante
by
dante.picchioni
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AFNI Message Board
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Pages: 123