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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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Hi Rick,
The recent change is more than sufficient. We're just at the "playing around" phase with these particular data so it will not be difficult to re-run them. Thanks for letting me know.
All best,
Paul
by
paulhami
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AFNI Message Board
Hi Rick,
Okay, thanks. Makes sense. And, sorry, I'm using data sent by a remote collaborator, so the residuals+tlrc is probably something we generated.
One follow-up: it looks like errts.anaticor has fewer volumes than were originally put through anaticor; I assume this is because of volume censoring. If this is the case, is there a way to keep the censored volumes for book-keeping pur
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paulhami
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AFNI Message Board
Hi Rick,
I wanted to follow up on this thread.
With our resting-state afni_proc script, we get three output files:
errts.anaticor.rest_Subject_1_Run_1+tlrc
errts.rest_Subject_1_Run_1.tproject+tlrc
residuals+tlrc
The tproject errts and residuals files are new to me but looking at the functionality of 3dtproject makes me think that the output of this function is the "cleaned"
by
paulhami
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AFNI Message Board
That is superior, Rick. Will update tomorrow and take it for a spin!
Paul
by
paulhami
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AFNI Message Board
Howdy Rick,
Thanks for your thoughts!
Yes, we do run into this about 15% of the time.
A list option for -tcat_remove_first_trs would be excellent. Let me know if/when?
All best,
Paul
by
paulhami
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AFNI Message Board
Hi AFNI gurus,
Using 3dttest++ with a single array covariate (age) and a voxel-wise covariate (VBM-derived indices of grey matter volume) to compare depressed and non-depressed groups with respect to a novel DTI measure (center = SAME for both covariates), we observed a nice between-groups difference. To further understand this finding, what we'd like to do is pull the residuals (i.e., th
by
paulhami
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AFNI Message Board
Where's the Like button on this site?
Well done, guys. Thanks, again, for all your hard work and thanks on top of that for the nonlinear option!
Paul
by
paulhami
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AFNI Message Board
Hi Gang,
Using a functional mask has helped immensely.
Thanks for writing this great program!
Take care,
Paul
by
paulhami
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AFNI Message Board
Ignore my last message. It was pausing because we overloaded our server. We're using a mask now to great effect.
All best,
Paul
by
paulhami
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AFNI Message Board
Hi Peter,
Whoa. Really liking 3dMVM. We've made a script that is running but it appears to have hit a long pause. Specifically:
Reading input files now...
If the program hangs here for more than, for example, half an hour,
kill the process because the model specification or the GLT coding
is likely inappropriate.
[1] "Great, test run passed at voxel (53, 95, 75)!"
[1
by
paulhami
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AFNI Message Board
We replicated the same problem with a different dataset and paradigm.
Good to feel consistent!
Paul
by
paulhami
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AFNI Message Board
Hi Gang (collectively and individually)!
Helping a friend with an analysis. We're using GroupAna in matlab to do a 3-way ANOVA (balanced Type 3; Group-by-Condition-by-Subject). It's a pretty straightforward design and analysis and runs all the way through (giving a status update about which slice it's processing, etc.). The issue is that it writes only a single, axial slice as o
by
paulhami
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AFNI Message Board
Salutations,
We've started working with some diffusion weighted data and, correspondingly, have acquired a new AFNI need (AFNeed). Looks like you already have some very fine programs for estimating cool parameters and conducting tractography. We're wondering about preprocessing tools. Specifically:
Coregistration across different gradient direction acquisitions. Specifically, cor
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paulhami
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AFNI Message Board
Hi Gang,
It gives a different error, at least:
[1] "-----------------"
[1] "Totally 61 slices in the volume data."
[1] "Starting to analyze data slice-wise. Running progression shown below:"
[1] "-----------------"
Z slice # 1 done: 03/06/14 12:51:49.570
Error in if (KHtest & all(resList$scl > tol)) outData <- outData[c(2, :
miss
by
paulhami
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AFNI Message Board
Hi all (mostly likely Gang),
We're getting the following error when we run 3dMEMA and our IT guys are stumped:
[1] "-----------------"
[1] "Totally 61 slices in the volume data."
[1] "Starting to analyze data slice-wise. Running progression shown below:"
[1] "-----------------"
[1] "Package snow successfully loaded!"
Z slice # 1 do
by
paulhami
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AFNI Message Board
Hi Rick,
Thanks much for your reply.
Just to make sure I'm getting you, if I were to lowpass at, say, .25 Hz and I have a TR = 2 sec then, in the context of lowpass filtering during regression, this would entail including only a single regressor that completes a cycle once every four seconds and I wouldn't be taking such a big hit in terms of df. Is that correct? If so, it might b
by
paulhami
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AFNI Message Board
Gurujis,
Let's say I'm doing subject-level analysis of a block design FMRI task and want to filter out high frequency fluctuations in the time series (e.g., blocks last 20 sec, TR = 2 sec, filter out fluctuations in BOLD at fastest possible frequency of .25 Hz) during preprocessing and then filter out low frequency noise with -polort A during regression. Provided doing this is advisa
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paulhami
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AFNI Message Board
...crickets...
Just wanting to open up this discussion. I won't hold anyone responsible for their opinion.
by
paulhami
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AFNI Message Board
Okay. Thanks Daniel! Will look into the options you suggest.
Thanks, again, to you and Peter for a beautiful template. Just played with it some more this afternoon.
by
paulhami
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AFNI Message Board
Greetings!
We are currently comparing manual to auto_tlrc normalization of child brains using the beta version of HaskinsPeds_Template very kindly provided by Peter Molfese and Daniel Glen. Wondering if you could let us know which AFNI environment variable to tweak to set the template volume to this new template when we're manually warping...easy to do with auto_tlrc; currently less clear
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paulhami
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AFNI Message Board
Fellow Travelers,
We're currently considering new analysis paths for task-based FMRI data and would like to hear your thoughts with respect to applying to task data the same denoising procedures that we might apply to resting-state data. As I understand it, the potential disadvantage of applying, say, the same denoising steps that are carried out in afni_proc example 5.c. would be loss of
by
paulhami
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AFNI Message Board