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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:
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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
Hi!
I have always been quite confused about when the errts-file is generated.
When running a resting state scenario with afni-proc (no stim files) I always get the errts-tproject or errts.anaticor file. This is because the command
3dTproject -polort 0 -input pb01.$sub_id.r01.volreg+orig.HEAD -censor motion_${sub_id}_censor.1D -cenmode ZERO -ort X.nocensor.xmat.1D -prefix errts.${sub_
by
Robin
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AFNI Message Board
Reviving this as well:
1. Do you guys recommend using ANATICOR with task data? It usually reduces effect sizes for us but that does not mean that it's not closer to the truth... We implement it in afni_proc.py by:
-regress_anaticor_fast \
-regress_reml_exec \
2. When having empty stimfiles (e.g. due to an event never occurring, like failing a certain task) you can prevent
by
Robin
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AFNI Message Board
Reviving this!
I'm also interested in getting the errts.tproject (or errts.anaticor) with the censored TRs removed instead of set to 0. Here is why:
For resting state fMRI where the errts.file is the file you want t to take to next step of your analysis (e.g. correlations) we preform an extra cleaning step using the data driven applecor function. We feed it the re-meaned errts-file to
by
Robin
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AFNI Message Board
I mean that sub-BRIK 4, 6 and 8 are not threshodlable. The interaction (sub-BRIK 3) is fine. 4, 6 and 8 are all the sub-BRIK right before the t-score sub-briks.
Thanks!
by
Robin
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AFNI Message Board
Sorry, the interaction was there (sub-brick 3). But still confused about the Interaction without the label. Here is the output:
Dataset File: bp_anaticor+tlrc
Identifier Code: XYZ_88YH5z4k40605p65tuJ85V Creation Date:
Template Space: TT_N27
Dataset Type: Func-Bucket (-fbuc)
Byte Order: LSB_FIRST
Storage Mode: BRIK
Storage Space: 3,456,000 (3.5 million ) bytes
Geome
by
Robin
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AFNI Message Board
Thanks!
Oh, so the gltCodes are not necessary, they only provide me with the t-scores...
No, I do not get an F-score. Or I don't think I do. I get, except the t-scores;
The Intercept (how should I intepret this and can I use it for something?)
The F-scores for Treamtent and Stim (These sub-briks are called Stilm F-score and Treatment F-score).
Two sub-briks for the interaction
by
Robin
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AFNI Message Board
Hi!
Running a factorial analysis using 3dMVM since my groups are uneven. First off, does my interaction set-up look OK? We have a patient group were some get treatment and some get placebo. We want to see the effect of the treatment when they are presented with two stimuli (one that should be affected by the treatment). I.e. the contrast between stim1 and stim2 should vary depending on real or
by
Robin
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AFNI Message Board
Thanks! Now it makes sense.
Follow up question:
1. Will it make a big difference to use 3dMEMA vs 3dttest++? When possible, should you always use 3dMEMA over 3dttest++?
2. We also use 3dANOVA3. Should we also replace that with 3dMEMA in some way? Or how do you include the reliability from each beta when you have a design where ANOVA is fitting?
Thank you,
Robin
by
Robin
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AFNI Message Board
Hi!
Assuming an experiment where the subjects get two different stimuli A and B. We are interested in the contrast between A and B: C=A -B.
Normally we would have run this via afni_proc.py and defined the contrast using:
-gltsym 'SYM: A -B' \
-glt_label C \
This would give each subject's stats file a sub-brik with the t-score from a t-test with null: C = 0 where C = A-B.
by
Robin
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AFNI Message Board
Thanks for the very detailed reply!
Yes, that is confusing... The used computer is a Windows computer that does not even have AFNI. It is running MobaXterm to connect to our redhat server with AFNI installed. How is it even possible to run an SHM connection there?
We will try witth the suggested flag (-NOshm)!
Thanks again.
by
Robin
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AFNI Message Board
Hi! After talking to Rick we decided that I should post this.
Some of our researchers are using 3dGroupInCorr and the AFNI viewer for trying to optimize DMN seed locations. They have experienced some issues with 3dGroupInCorr closing the connection randomly. This can occur after just 1 click or 20 clicks and might happen 1-2 times a day. AFNI is installed on a remote server and accessed via ss
by
Robin
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AFNI Message Board
Thanks for the input Bob! It feels good to have an explanation!
We are, compared to the NIH, very small and do not run a huge cluster. We have two separate quite capable Linux servers (I guess this would correspond to two nodes at your place). A relatively large Windows storage server is mounted on each of these and this is the location on the servers where people do their analysis (since that
by
Robin
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AFNI Message Board
Hi!
I have AFNI locally on my desktop computer and on our analysis servers. The analysis servers gets their large storage space by mounting a our storage server on them. This is a bit of a trade off since it is very expensive to have a huge powerful server that also have vast amounts of disk space. But on the other hand files sometimes have to travel through the network and that might slow som
by
Robin
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AFNI Message Board
Hello AFNI experts.
We are currently optimizing our task based analysis and are trying out different ways to include physiological data. For resting state analysis we preformed an ordinary afni_proc.py script (with ANATICOR and RICOR) and cleaned up the resulting .errts.anaticor file even further by e.g. using the rvhrcor method. This was quite straight forward since the regressors created by
by
Robin
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AFNI Message Board
Hi!
Thanks! I just realized that the stats.REML file had all my contrasts! But the standard (3dDeconvolve) stats file does also have my contrasts and it seems like the regression is run there as well. Are you absolutely sure that the regression is also not preformed in the 3dDeconvolve part? The proc script does have the large 3dDeconvolve part with all stimfiles and outputs it to stats.$subj.
by
Robin
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AFNI Message Board
Let me revive this!
We want to use ANATICOR in our task based data analysis but I don't see how it helps me? I realized that the ANATICOR part is run after 3dDeconvole (I guess that is what Rick mean with 3dREML.fit). So how is this helping me, the ANATICOR info is not in the big regression? I want my stats output to be cleaned from the noise that ANATICOR takes care of (spatially varying
by
Robin
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AFNI Message Board
Thanks guys! Real good info.
A perhaps silly question, just for my sanity: How does AFNI know what "TT_Daemon" is? When I put it into a function similar to what peter suggested:
whereami -mask_atlas_region "TT_Daemon::left_amygdala -prefix amy
TT_Daemon is not a function in abin and it is not a script in the current directory. I mean, it is an atlas but it is kind of used as
by
Robin
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AFNI Message Board
Hi!
So I know you can create ROIs by going to plugins and select Draw Dataset. There you can "Choose Atlas" and then region.
Problem 1: When clicking on the lists of regions all of them are displayed. Even if I have a huge screen a couple if rows (about 4 for my screen and about half if you run a laptop) are not visible since they are below the screen. This is problematic if you w
by
Robin
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AFNI Message Board
Sure!! But the wget command still does not work even though I can access this message board.
by
Robin
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AFNI Message Board
Do I understand the current recommended approach?
Designs allowing t-tests
Here we can use the 3dttest++ function with the -Clustsim option. Is this the way to do it?
3dttest++ -prefix output_name -mask mask_sim+tlrc -Clustsim \
-setA \
sub003.results/stats.sub003+tlrc'[1]' \
sub007.results/stats.sub007+tlrc'[1]' \
etc...
Where the mask is the TT_N27+tlrc. mask re
by
Robin
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AFNI Message Board
Hi again,
I have now successfully updated afni to version 16.2.09 using the -local_package method. The binaries from the page was updated even though the version displayed on the page was old.
Regarding the proxy problems: We have had some problems accessing the afni pages, such as the function help pages and this message board. When trying to get to an afni page it takes forever but eventu
by
Robin
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AFNI Message Board
The version on the website is said to be:
Note
The current latest and greatest version of AFNI is: 16.1.13
But when running afni -ver on my updated system is says 16.2.09. That is why I did not try the -local procedure! I'm I missing something?
When running the suggested wget command I run into (I think) the exact same problem (both servers and my desktop):
# wget
--2016
by
Robin
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AFNI Message Board
Hi AFNI people!
I'm trying to uppdate the current version of AFNI running on our analysis servers (and my local computer) while connected to a network using a proxy for internet access. This have worked in the past but I can no longer get it to update! The same problem occurs on both analysis servers and my local computer. The proxy is fine since I can both use a browser and install packa
by
Robin
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AFNI Message Board
(I edited the previous post).
But I guess it is "solved" but I'm not happy about it. I would like to be able to reproduce the error so that I can fully understand it. Beacause now I can run it without fail with both +orig.* and .nii files, even though they give slighly different results (in warping costs etc).
I have run a lot of permutatons of the settings and I'm still
by
Robin
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AFNI Message Board
Hi, I edited my previous post. I'm trying to reproduce the .nii error but I'm not successful at this moment.
As I mentioned in the previous post: Is it possible that the script I used as a template (the other lab's script), that was sent by mail and proabably landed at a windows computer at some point, had some formatting errors? Even tough it did not complain about line-endings
by
Robin
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AFNI Message Board
Did some more digging:
I used one of my older scripts (with the same proc-settings) and it worked. I started to look some more into it.
1. Without @Align_Centers prior to afni_proc the analysis fails at the anat_w_skull warping
2. It does seem to matter if I give @Align_Centers the input files as .nii or as BRIK and HEAD. For example when first doing
3dcopy data.nii .
I get the data as
by
Robin
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AFNI Message Board
Major edit. Removed all the old text.
I ran all the steps individually and everything seemed sucessfull.
My collaborator sent me their script which I used as a template. It might have been some formating error on that one (even though it did not seem that way - You usually get errors about row endings in that case). When I ran dos2unix on it, it seems to work...
This might have been a co
by
Robin
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AFNI Message Board
Hi again, so I ran a couple of different settings. First of all I tested running with just linear warping and that works, even without running the 3dAlignCenters function prior to the analysis script.
Then I tried a couple of different cost functions and non-linear warping by running 5 different afni_proc sricpts with these settings:
1.
-align_opts_aea \
-giant_move \
-cost lpa \
by
Robin
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AFNI Message Board
Hi Rick!
This is my comnand:
@Align_Centers -base ~/abin/TT_N27+tlrc. -dset TEST_sT1W_3D_TFE_SENSE_4_1+orig. -child TEST_Risk_SENSE_8_1+orig.
So yes, I use the template, which worked last time I had the same error!
by
Robin
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AFNI Message Board
Thanks, I will!
Just to make sure: Is it the "align" block or the "tlrc" block that is failing? Since you wrote that the "affine alignment" probably is not working properly (might be confusing affine alignment and the affine warping?). Or is it the align part that is troublesome but it is noticed when 3dNwarpApply tries to apply the warping to the "broken&quo
by
Robin
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AFNI Message Board