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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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I'm bumping this to see if someone could please help me with these two questions. To summarize, they are:
1) Why does 3dttest++ change the temporal degrees of freedom when -etac is invoked?
2) Why would including multiple hpows when -etac is invoked produce significant clusters that don't pass correction for any hpow setting alone?
I'd be happy to provide some data if that w
by
asali
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AFNI Message Board
Hello,
I am using ETAC in 3dttest++ and have a couple of questions I posted a few months ago, but didn't get a response.
1) I've noticed that the stats file that 3dttest++ outputs with -etac turned on has slightly different z-scores than if I run 3dttest++ without -etac but instead use just -toz or -clustsim. I poked around in the source code and I think it is because of a subtrac
by
asali
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AFNI Message Board
Thanks so much, Rick. I saw this used in some older posts on the message board. Here's the link for one:
It sounds like those previous users didn't need to provide -surf_B. Is that correct? Thanks again!
-Anthony
by
asali
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AFNI Message Board
Hello,
Is there an advantage in SurfSmooth to passing multiple surfaces using the -surf_A, surf_B commands. In the afni_proc generated example, -surf_A is used to specify the smoothwm surface. I have seen some examples where both smoothwm and pial are passed with surf_A and surf_B, respectively. How does the program behave differently if two surfaces are given instead of one. I've pasted
by
asali
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AFNI Message Board
Hello! I would like to make sure I am understanding the default settings of 3dTshift correctly. I'm working with data that I have run through fmriprep so that tzero is not set to 0 as in afni_proc.py. Based on some other posts on this board, I believed I needed to subtract ~1/2 TR from my onset times to make the model in 3dDeconvolve reflect the slice time corrected data. It was my understan
by
asali
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AFNI Message Board
I never received a response to this question and I'm still really confused about how to interpret the results. When I use a single hpow value in ETAC (0,1, or 2) for some contrasts, I do not get any significant clusters. However, when I use a combination of hpow values as in the command below, I do get significant voxels.
-ETAC_opt NN=2:sid=2:hpow=0,2:pthr=0.01/0.001/19:name=h1:fpr=5 -
by
asali
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AFNI Message Board
I'm sorry for the double post. I just noticed a mistake I was making, but I'm still a bit confused. My 3dttest++ command above should have been the version I've pasted below. When I fixed this, I now have no voxels that pass the correction for hpow=0, hpow=1, or hpow=2 when tested separately. However, when I run -ETAC_opt NN=2:sid=2:hpow=0,1,2:pthr=0.01/0.001/19:name=all:fpr=5 I ge
by
asali
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AFNI Message Board
I am new to using ETAC in 3dttest++ and I have a question about the hpow value. In a dataset I'm currently analyzing, when hpow is set to 0, I get cluster activity that makes sense and is in line with what -Clustsim in 3dttest++ gives me, but when hpow is set to 1 or 2, no voxels pass the correction. Could someone help me to wrap my head around what that means? I've pasted my full 3dtte
by
asali
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AFNI Message Board
Hi all,
I noticed today while running some analyses that the z-statistics produced when I run 3dttest++ with -Clustsim differ very slightly from those produced when I use -ETAC instead. I must be misunderstanding, but I expected both to be the same up to when the permutations start. I've pasted my 3dttest++ command below. The only difference between the two commands is using -Clustsim o
by
asali
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AFNI Message Board
Hello. I have a question about the regress_censor_motion option in afni proc. In example 6 of the afni proc help, the motion threshold is set to 0.3. What is the appropriate unit of measurement for this threshold? Also, how does this relate to the statement in the explanation that says "censor TR pairs where the Euclidean Norm of the motion derivative exceeds 1.0." Thank you so muc
by
asali
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AFNI Message Board
Hello. I've noticed that several of the afni_proc examples use -volreg_align_e2a such that the inverse of the transform from aligning the anatomical image to the EPI is applied along with motion correction. What are the important factors when deciding whether to just align the anatomical to the EPI or whether to add in -volreg_align_e2a. Thank you!
-Anthony
by
asali
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AFNI Message Board
Hi Ziad,
The scan does not have a lot of neck coverage and I have not been able to identify any other reason why it is failing. Would it be possible for me to upload the scan for you to see?
Thanks again!
Anthony
by
asali
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AFNI Message Board
Hi. I am attempting to use 3dSkullStrip with an mp2rage image. While 3dSkullStrip is running, I receive several warnings about self-intersecting surfaces. The resulting output consists of only the midbrain and white matter surrounding the midbrain. The non-stripped image does not appear to have shading. I have tried adjusting the options in 3dSkullStrip, but I have not been able to improve t
by
asali
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AFNI Message Board