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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
Thanks Rick!
Yes, this was our first thought too so we made a clean directory. Just to confirm I re-ran it with 2 new folders called "affine" and "NL" where one has the -tlrc_NL_warp setting and the other don't.
My current AFNI-version:
afni -version
Precompiled binary linux_ubuntu_16_64: Feb 18 2020 (Version AFNI_20.0.10 'Galba')
My ubuntu-version
by
Robin
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AFNI Message Board
We tested the new binaries this morning and running the script I attached worked, we can complete the pre-proc and the output stats looks reasonable! Thank you for a fast fix.
However, there is still a FATAL ERROR that without "GOFORIT 6" probably would have stopped the pre-proc.
The error is still under @Align_Centers:
Performing center alignment with @Align_Centers
++ 3d
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Robin
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AFNI Message Board
Since I'm in Sweden my day was almost over when you replied =).
Just let me know when I can download the new binaries! Did you manage to reproduce the error?
Thanks a bunch for all this amazing support.
by
Robin
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AFNI Message Board
Hi and thanks!
I did screw up, I pasted my previous installation command and that was on a CentOS system. I removed the abin directory completely, downloaded the source from here due to proxy-issues. Then I went to my local home-folder and ran
curl -O
Followed by
tcsh @update.afni.binaries -local_package /home/robka/linux_ubuntu_16_64.tgz -do_extras -bindir /usr/local/abin
Unfortuna
by
Robin
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AFNI Message Board
Hi, Robin-
I am going to split this into a new thread, as it is a separate question from here (where it was originally posted):
I have also edited the subject line to reflect the first error shown in the output.
Hope that is all reasonable.
(Heading into work now, will reply more anon, or perhaps someone else will chime in first.)
-pt
-----------------------------------------
by
Robin
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AFNI Message Board
Thanks!
I could only find this part regarding libgsl.so in the installation guide (Ubuntu18):
sudo ln -s /usr/lib/x86_64-linux-gnu/libgsl.so.23 /usr/lib/x86_64-linux-gnu/libgsl.so.19
That does not cover linking libgsl.so.19 (or libgsl.so.23) to libgsl.so.0.
The installation guide worked nicely when I installed AFNI and this libgsl.so.0 issue surfaced after I updated AFNI. Prior to the upd
by
Robin
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AFNI Message Board
I found another answer from Paul Taylor and that fixed it. Sorry, I can't delete this but perhaps it will help someone else.
Solution:
sudo ln -s /usr/lib/x86_64-linux-gnu/libgsl.so.19 /usr/lib/libgsl.so.0
by
Robin
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AFNI Message Board
Hi!
I updated AFNI om my ubuntu 18 machine:
Precompiled binary linux_openmp_64: Feb 14 2020 (Version AFNI_20.0.09 'Galba')
I ran
afni_system_check -check_all
And ran into some expected problems (like an R-package missing due to, I presume, new functionality). But the real problem here are these errors:
testing ability to start various programs...
afni
by
Robin
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AFNI Message Board
Hello Gang!
This might be a silly question, but I was intrigued when reading about BayesianGroupAna.py. Especially since you emphasise that the standard approach can be very over-penalizing. I just don't know what part of our traditional analysis pipeline that could be replaced by this (for both resting state and task fmri). I don't seem to see that you input any brain data into this
by
Robin
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AFNI Message Board
Hi!
We are getting both a CPU cluster and a rack/set of GPUs to our lab. The CPU cluster will help with the time consuming non-linear warping since this process can be spread out over multiple threads. Could other process (or even non-linear warping) like 3dDeconvolve run on GPUs instead? I know you usually need different code for a process to run a GPU but it is worth asking!
Can we improv
by
Robin
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AFNI Message Board
Hi!
I have been thinking about the scale block, which I have never used. As far as I understand, it should not affect the final statistical group maps of e.g. a task where we compare the beta values. But it would affect the averages of an ROI.
For resting state seed analysis, is it important to use the scale block? We would e.g. use a DMN seed, for each subject take the average time course
by
Robin
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AFNI Message Board
Thanks to both of you, really!
I think I have enough now to go ahead :). This will be a helpful thread to re-visiit!
Many thanks,
Robin
by
Robin
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AFNI Message Board
Hi Paul,
Thanks for your input!
Great regarding the cluster sizes and that I have got the correct sources for citation!
Regarding running two 1-sided t-tests: We almost always use the 2-sided tables that are generated from clustsim. Perhaps we can get away with a 1-sided on some of our tasks but we have chosen to basically always use 2-sided since we are interesed in differencies in both
by
Robin
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AFNI Message Board
Thanks Gang!
This leaves a, for now, final set of questions.
1) The "currently considered acceptable threshold" I get form the Bob's power-point presentation and from these two papers:
fMRI clustering and false-positive rates.
FMRI Clustering in AFNI: False-Positive Rates Redux.
From here I gather that one should use no p-value greater than 0.002. Is there any new info/pap
by
Robin
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AFNI Message Board
Thank you so much Gang!
Feel free to step up to the soap box any time...
Then we will give the rare p < 0.002 (0.001) findings extra weight but we will not through away anything interesting at the higher p-values (e.g. 0.005 with corresponding threshold).
The annoying thing is that it is nice to be able to write "multiple comparsion corrected" in a paper. For example SPS jus
by
Robin
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AFNI Message Board
Hi!
I guess this is the 100th post regarding this matter but maybe there is now some new info out there.
I really appreciate how thurough you guys have been in really addressing the issues that surfaced post the Eklund paper (he is actually my PhD co-supervisor). And as far as I can tell your approach is to reach a theoretically "true" false-positive cluster rate of 0.05 when all
by
Robin
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AFNI Message Board
Great, then in the future I don't have to bother with extra scripts, just use afni_proc and tell it to use the mask_epi_anat and no detrend ;) and just make a script that extracts the acf from each and average them.
Thanks Rick!
by
Robin
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AFNI Message Board
Just adding in (same lab)
In a "normal" 3dttest++ scenario we e.g. test if two groups differ (in beta values) and we get a significant cluster. From this cluster we extract the betas (the same betas the 3dttest used to get a significant cluster) so that we can make nice plots (and if it's an ANOVA we can do post-hoc). These betas should, of course, also produce a significant dif
by
Robin
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AFNI Message Board
Thanks Rick!
I probably can't use the pre-proc acf parameters anyway since we, in the end, want to use a group mask based on the mask_epi_anat mask from all subjects only including voxels that all share (i.e. the union mask) via
3dmask_tool -input mask_epi_anat.*+tlrc.HEAD -prefix mask_epi_anat -frac 1
Then we preform a separate script for 3dFWHMx. If we use the acf from the pre-proc
by
Robin
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AFNI Message Board
Hello,
I have previously created ROI:s using e.g.
Make ACC mask named ACC_mask
whereami -prefix ACC_mask -mask_atlas_region 'TT_Daemon::ACC'
Make Insula mask named insula_mask
whereami -prefix insula_mask -mask_atlas_region 'TT_Daemon::insula'
I think the whereami command is kind of complicated and I get stuck now that we have swapped to the MNI152_2009_template.n
by
Robin
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AFNI Message Board
Hi Gang and thanks!
I posted a question here but I kept using google during the mean time. I have no idea why, but these particular settings did the trick for me in the /usr/lib64/R/etc/Malkeconf file. I had to include -fpic in both the 1st and 3rd option. I have no idea why this worked or why I did not have a ~/R/Makevars file or why my changes to ~/R/RcppEigen/skeleton/Makevars was not pick
by
Robin
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AFNI Message Board
Thanks Gang, I saw that when troubleshooting. But I can't seem to make it work. It feels like R does not find what's in the file since, for every thing I have tried, I still get
Error in .shlib_internal(args) :
C++14 standard requested but CXX14 is not defined
First off all, I only found the Makevars file here (not in ~/R/Makevars):
~/R/RcppEigen/skeleton/Makevars
The file loo
by
Robin
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AFNI Message Board
Hi!
Preforming a fresh AFNi-install on CentOS which I have never worked on. The instructions worked great!
The only thing not surviving the afni_system_check -check_all is one R-package: brms. The rest were installed with rPkgsInstall -pkgs ALL.
I have tried some solutions I found online but with no success. This is the error message, any ideas?
> install.packages("brms"
by
Robin
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AFNI Message Board
Hello Bob and thanks for such a detailed reply!
1+2) On that you would not recommend 3dFWHMx -detrende for already processed data:
That is interesting since afni-proc seems to preform smoothness estimates with the -detrend option per default.
My afni version is brand new:
afni -ver
Precompiled binary linux_ubuntu_16_64: Dec 4 2018 (Version AFNI_18.3.13 'Augustus')
In my afni-p
by
Robin
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AFNI Message Board
Hi! Sorry for a multi-question post but since they are related I felt bad posting several separate posts.
I have tried the different approaches to apply multiple comparisons error corrections and ran into some questions:
1) Approach1: 3dFWHMx + 3dClustSim. Detrend?
To use 3dFWHMx -acf -mask GM+tlrc. with our without -detrend does, according to the documentation depend on if your data has
by
Robin
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AFNI Message Board
This is really informative.
Yes, I want to analyze their data and run fwhmx + 3dclustsim (this method seem to be a bit less conservative compared to 3dttest++ -clustsim or -etac) and see if we ge the same results.
I suspect that using pars of 1-sided t-test have been used.
Is that when e.g. you have two conditions (e.g. iaps images and shapes) and two groups (controls and patients) and y
by
Robin
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AFNI Message Board
That is perfect... We were trying to re-create some old results and tried bandpass (since we lost the original script). We use bandpass for resting state but not for task (any more).
How can I be sure I'm not using using global signal regression? It is across all voxel average signal right? As far as I can see we don't use it.
We are, in a way, demeaning since we use polort A (usu
by
Robin
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AFNI Message Board
Thank!!
So, just to make sure I get this right.
I do get these datasets:
stats.sbj_A_+tlrc. = Normal stats file based on linear regression. Betas + t-stats where t-stats are not taking temporal auto correlation (important for singlesub)
errts.sbj_A+tlrc = The residuals (error-time-series), variance not accounted for in the model above
stats.sbj_A_REML+tlrc. = In this context it'
by
Robin
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AFNI Message Board
Ha! Sorry if it sounded charged.
We are an AFNI lab and we really like "the AFNI way", it makes us feel in control when we can avoid toolboxes that simply spit things out for you (that we think look a bit toooo good).
The reason for me asking so bluntly is that it's frustrating when we keep seeing reasonable findings disappearing when applying corrections while similar tasks
by
Robin
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AFNI Message Board