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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
Page 7 of 7
Pages: 34567
Results 181 - 198 of 198
Thanks!
I initially used giant move but also tried ginormous.
Okey, I will try different settings on monday. But if I only do affine warping it does not fail, it completes with minor cropping of cerebellum. This is not fixed by init_xform center like it was last time (my old post)...
How come that their scanner places these volumes so far appart? Is it common?
by
Robin
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AFNI Message Board
Hey AFNI experts,
I have basically posted this exact question once before. My afni_proc.py script kept dying during one of the warping stages (applying warp using 3dNwarpApply) giving me a Fatal Signal 6 (SIGABRT) received and a memory corruption message.
We figured out it was due to a large distance between the anatomical and functional datasets. The problem was solved by running @AlignCen
by
Robin
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AFNI Message Board
Hey AFNI Gurus!
We just got our Siemens Prism installed and the possibilities of simultaneous multi slice (SMS) / multi band (MB) imaging just opened up to us (SMS and MB is the same thing, right?). We are used to evaluate fMRI scan settings and comparing different coils using tSNR maps. If I remember correctly these tSNR maps should represent the average signal divided by the average noise be
by
Robin
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AFNI Message Board
Hi!
I have been reading about how to obtain the final table of p-values and cluster sizes such that family wise errors are taken into account. I realize that I need to use 3dClustsim in combination with 3dFWHMx: This seems to be the latest bid. And I know this is a work in progress, much like is suggested by Bob's reply in this thread:
So I know things can change. But, I would just
by
Robin
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AFNI Message Board
Thanks! :)
I have one final set of questions regarding this particular design (as described in the first post). We do have 20 subjects and all of these 20 are associated with both levels of the DRUG factor (they all got both Drug and one Placebo). But only 10 of them are associated with the each level of the GROUP factor (which background the drug was paired with). So, should -clevels be 10 or
by
Robin
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AFNI Message Board
Super, thanks Gang!
Quick follow up: Why type 5 and not type 4? Both have Fixed Fixed Mixed.
Don't think I fully grasp the meaning of "nested"..
And would you mind elaborating why group is a fixed effect? Thougt it was random since it is "random" which group they end up in.
by
Robin
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AFNI Message Board
Hello AFNI board,
I have ended up working with a, for me, non-trivial design and I need help with the group level analysis. Especially the ANOVA aspect.
The design (not mine) is like this:
We have 20 subjects which are conditioned by giving them, in two sessions, a drug in combination of viewing a certain picture and a placebo when viewing another picture. To balance this the background coup
by
Robin
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AFNI Message Board
Big thanks! This worked, finally! Both for affine and -tlrc_NL_warp.
But why did it not work by moving only T1 to the center for the EPI? Shouldn't that be enough? I.e. my second @Align_Centers suggestion. This would have moved the center (not aligned) of the T1 to the center of the EPI volume and they should have been close enough?
by
Robin
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AFNI Message Board
Thank you Daniel!
Just to make sure:
1. So it SHOULD work to remove the "-tlrc_opts_at -init_xform CENTER" option and to run @Align_Centers insead for the linear warping as well?
2. For the non-linear warping I should run @Align_Centers. Should I use the template as the base or the functional data?
@Align_Centers -base ~/abin/TT_N27+trlc. -dset T1+orig -cm
or
@Align_Cente
by
Robin
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AFNI Message Board
Hi AFNI!
I ran into some trouble with a dataset where the anatomical and functional datasets were separated by a great distance (at least 60 mm). This caused me to get warping errors:
Linear warp: Script completed but parts of the brain were cropped out
NL warp: Script crashed due to memory corruption. Error message:
++ 3dNwarpApply: AFNI version=AFNI_16.0.05 (Feb 10 2016) [64-bit]
++
by
Robin
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AFNI Message Board
Thanks Rick! Then we will be using dcm2nii from MRIcron instead.
Is this a potentiall feature to be added in the future since I guess 4D DICOMs will be more common? Would be really nice to be able to stick with afni for everything and avoiding mixing in other softwares.
I do not know when this was implemented but I guess Philips did this? Do you think this setting can be changed? You are ri
by
Robin
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AFNI Message Board
Hello crew of AFNI!
We have script for converting DICOM files to NIFI files. We got it from another site (acutally NIH) where it has been working fine. This script uses Dimon to convert the DICOM files to a NITFI file. I think that Dimon expects the inout DICOM data to be of one file per slice, like it usually is with DICOM images. However, we only get one large 4D DICOM file when we export th
by
Robin
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AFNI Message Board
Thanks again Rick!
I'm still a bit confused about BLOCK(5) and BLOCK(5,1).
First off, I thought the BLOCK(5) function that was generated by convolving a square wave of widht 5 s (a boxcarfunction, BLOCK, height 1) with and a gamma function? At the location of the ONSET in the stimfile. Or what did you mean with "BLOCK " in
"BLOCK(5) is generated by convolving the si
by
Robin
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AFNI Message Board
Thanks Rick!
2. I might have been confused when asking. I guess the coefficients of the main effects are the betas. Any contrast that we create will not be a beta per see, but, e.g., a subtraction of two betas (C = B2-B1 ). But please, do explain BLOCK(5) vs BLOCK(5,1) if you have the time - that is another thing I have been thinking about.
Writing this post made me think of another questio
by
Robin
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AFNI Message Board
Hey AFNI crew!
I have a question best explained by a scenario. Imagine we have preformed a simple MID-task experiment. For simplicity we only focus on the feedback part: win_$5, win_$10, lose_$5 and lose_$10. In the future it would be interesting to look at contrasts between winnings/loosing different amounts (e.g. win_$10 vs win_$5) but for the moment let's imagine that we only have a co
by
Robin
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AFNI Message Board
Big thanks! Happy I aksed!
Are all packages updated with the same frequency? I mean, some times you do update functions (not that long ago uber_subject was changed so that the censored volumes in errts.anaticor was kept - for book keeping - instead of beeing removed).
I will send you the output as soon as I have installed it! Since it is a server that will be used by users the server conta
by
Robin
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AFNI Message Board
Hi!
We just installed a RedHat server to be used for our fMRI analysis so I obviously want to install afni. I have previously done this on my Ubuntu system and from (http://afni.nimh.nih.gov/afni/download/afni/releases/latest) downloaded the Linux OpenMP 64bit function package.
I never really understood the difference between these function packages and since it worked fine I just carried o
by
Robin
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AFNI Message Board
Hi, first time poster here!
My name is Robin and I'm visiting NIH from Sweden this week to, among other things, start learning Afni. I'm an MRI physisist but I have not previously worked with fMRI/fMRI-analysis, so I have spent these couple of days trying to get started since fMRI analysis will be a part of my job in the future.
My current status is that I'm trying to preform
by
Robin
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AFNI Message Board
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Pages: 34567