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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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Results 1 - 30 of 74
Greetings, comrades--
How would you recommend estimating smoothness in fALFF data for plugging smoothness parameters into 3dClustSim? Specifically, what kind of images should we apply 3dFWHMx to in order to get smoothness params? If we were using seed-based connectivity maps, the appropriate images would be the residual images.What is the most appropriate analogy to residual images for fALFF m
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paul.hamilton
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AFNI Message Board
Hi Gang--
Sorry for my late reply. Just getting back online following the holidays.
Thank you for turning me on to 3dRegAna. I just went over the manual. What a nice and flexible tool. The process you present implements the same approach I had in mind but much more elegantly. I also like how one can play around with different models...
Thanks, again, for the help!
Paul
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paul.hamilton
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AFNI Message Board
Hi Gang--
Following up...
QuoteHowever, you may consider using 3dttest++ or 3dRegAna for your next question.
Do you have suggestions for how to implement a shared-variance analysis with 3dttest++ or 3dRegAna?
I would think it could be done with just 3dMVM, with a little work beforehand in Matlab or Excel. For example, say we have predictor variables X and Y that are correlated and we w
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paul.hamilton
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AFNI Message Board
Thanks, Gang. The Venn diagram-based discussion was really nice.
One addition thread:
For each of the qvars, is it possible to get 3dMVM to output a t- or r-statistic?
Thanks much!
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paul.hamilton
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AFNI Message Board
Greetings, venerable AFNIstas-
I'm new to the 3dMVM game so please feel free to direct me to a previous thread if you've already answered this. Just want to make sure that our coding matches our questions.
We have two quantitative variables per subject: 1) CSF concentration of the dopamine metabolite homovanillic acid (HVA); and 2) age, which tends to be weakly but significantly c
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paul.hamilton
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AFNI Message Board
Greetings, Daniel--
At last circling back to this conversation and trying out your proposed fixes. I'm actually going to try out all of them on the full set of difficult data and see which one wins. In this context, three questions / requests for clarification emerge:
First, I'm assuming that T1_ns.nii means the SkullStripped T1?
Second, what does epi_am_un.nii.gz refer to?
Thir
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paul.hamilton
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AFNI Message Board
Greetings, Daniel--
Thanks so much for diving into our alignment problem. Much appreciated! We'll unleash your fixes on the data and will report back with the results early in the new year. The Dice coefficient we've been using is the one that gets reported in the summary text file generated by afni_proc.
More before too long...
Until then, happy holidays...
Paul
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paul.hamilton
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AFNI Message Board
Greetings Dear AFNIstas--
With the advent of @SSWarper in addition to some tricks with zero-padding and centering that you've kindly provided, the quality of alignment between our BOLD and anatomical data has improved dramatically. The approaches you've provided are also robust. For data from a 1500-subject, 15-site data consortium with which we collaborate, data from 13 of 15 sites
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paul.hamilton
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AFNI Message Board
Comrades--
We'd like to do some multi-voxel pattern analysis using data from a simple block-design study with baseline epochs long enough for the HRF to settle. One fork in the decision tree for implementing this approach is whether to use for training and testing a series of betas from individual blocks of each condition (using, e.g., 3dLSS) or to use the preprocessed BOLD time-series. W
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paul.hamilton
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AFNI Message Board
These are good scattered ideas, Daniel. Thank you. I'm going to get serious about these data this week and will report back...
Attaching a 3D rendering of subject with phantom for your viewing displeasure.
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paul.hamilton
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AFNI Message Board
Greetings, venerable AFNIstas--
Short but potentially challenging question: We are acquiring a series of dynamic t1 images. In each dynamic are the head of a living human and a gadolinium phantom that we're using for drift correction. Both move somewhat independently over the ~25 minute dynamic t1 sequence. This requires conducting and applying to the same images volume registration of bo
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paul.hamilton
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AFNI Message Board
Hi friends:
Please let me know if you have or are a promising student looking for a postdoctoral fellowship? I'm looking for someone interested in investigating mood and anxiety disorders at the intersection of molecular and neural levels. Examples include polygenetic neuroimaging and linking CSF-derived neurochemical alterations with structural and functional abnormalities in the brain.
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paul.hamilton
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AFNI Message Board
Just right, Rick! Many thanks! I'll apply generously to the data...
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paul.hamilton
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AFNI Message Board
Hi Rick--
"1. The correspondence won't be great, as the dice coefficient mostly shows whether the masks are approximately on top of each other. Since the coverage tends to differ, it mostly just shows whether there was a gross failure."
Do you have a Dice coefficient criterion for gross failure?
"2. Sure, I will look into adding it for the anat/template. Okay, that is
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paul.hamilton
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AFNI Message Board
Sri Gurujis-
We really like the new QC options you've made available via afni_proc. Two questions emerge:
1. Might we expect to see a correspondence between the qc_00_ve2a_epi2anat.???.jpgs and the "anat/EPI mask Dice" coefficient generously provided in the out.ss_review.*.txt file? I don't see documentation pointing to what the Dice coef is but I'm assuming it'
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paul.hamilton
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AFNI Message Board
Hi Gents--
I'm very with you in spirit here and I think this is a step forward but something turned out funky with the implementation. Mind taking a look?
Original volume = t1_dyn_contrast_volreg_ave.nii
Command = 3dWarp -deoblique -prefix t1_dyn_contrast_volreg_ave_DO.nii t1_dyn_contrast_volreg_ave.nii
See picture for pre and post (dyn_contrast_volreg_ave.nii on the left and t1
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paul.hamilton
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AFNI Message Board
Greetings--
Potentially "heady" in the header sense question for you.
At the scanner, on the same scout scan, we Rx two scans. One is a high-res SPGR and the other is an oblique slab of dynamic T1s. When we get back to the lab we convert the data to NIFTI via either dcm2niix or dimon and then overlay the oblique T1 scan on the SPGR in the AFNI viewer. We note that the oblique T1 i
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paul.hamilton
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AFNI Message Board
Hey Peter--
Still looking interpolation-y.
I ran:
3dAllineate -base anat_ns.nii -input t1_dyn_contrast_volreg_ave_zp_ns.nii -master t1_dyn_contrast_volreg_ave_zp_ns.nii \
-prefix t1_dyn_contrast_volreg_ave_zp_ns_al.nii -1Dmatrix_save t1_dyn_2_spgr.1D -cost mi -final wsinc5 -source_automask \
-autoweight -twopass -warp shift_rotate -verb -overwrite
where:
anat_ns.nii = high res whol
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paul.hamilton
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AFNI Message Board
Thanks much, Peter. Traveling now but will try once I'm back at my desk...
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paul.hamilton
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AFNI Message Board
Hi Peter--
Just got through trying out your approach and it looks really nice. Everything lines up. One remaining issue, though, is that some blurring gets introduced into the -input image during alignment to the -base. Is there a way to avoid this?
Many thanks...
Paul
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paul.hamilton
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AFNI Message Board
Many thanks, Peter. Looks really nice. I shall implement.
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paul.hamilton
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AFNI Message Board
Received and replied with a link to the data. While there was a confirmation of the reply being sent to you, I don't see anything in my SentMail folder so I'm confirming via this route.
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paul.hamilton
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AFNI Message Board
Hi Peter--I've been playing with your recommended approach and have achieved some cool looking but not-so-useful results. Perhaps you wouldn't mind taking a look? Feel free to let me know where you'd like me to send the data when you get a minute.
Many thanks...
Paul
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paul.hamilton
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AFNI Message Board
Thanks, Peter. It's after work hours here in Sweden but I'll try tomorrow and report back.
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paul.hamilton
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AFNI Message Board
AFNI gurujis--
My goal is use the -tpattern @filename option within afni_proc to do slice-time correction using the slice timings provided in a BIDS .json file. I've managed to confound my efforts in two easy steps:
First, read slicenums lines from a BIDS format .json file to get the slice-timing for the EPI data. Dump it into the 1D file slicetimes.1D
# first set a variable
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paul.hamilton
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AFNI Message Board
Hi guys--
Sorry to butt in, but Peter and/or Paul, I'm wondering if you recommend a similar approach to the above for getting optimal alignment between full and partial structural images? Say, for example, if Ruyuan wanted to get the best alignment between his high-res T2s and whole brain SPGR... In our case, we're doing dynamic T1 imaging using Gadolinium and would like to have the
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paul.hamilton
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AFNI Message Board
Howdy--
It seems that the case for multimodal parcellation (e.g., ) gets better and better:
--
--
...not to mention how well your new ROI-based, Bayesian approach works in this context.
We're wondering, then, if you have under development an AFNI-based facility for doing such parcellation? No problem if not as the Van Essen group's code is available, we'd just like to &q
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paul.hamilton
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AFNI Message Board
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