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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 guys,
I've used afni_proc.py to process gas challenge fMRI data. The original 3dDeconvolve model includes 6 motion derivative regressors (no gas stimulus regressor) and the errts output is then fed into an in-house software for further analyses. This software prefers time series not to be centered around 0. I've used -polort -1 to not detrend, and thus demean the time series, with
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nic
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AFNI Message Board
Hi Rick,
I've got another puzzling problem that may shed some light.
I've modified the 3dDeconvolve cmd in the original proc script to use a different stimtimes file and try a different response model (saved as a new script and chmod 777 newscript). This modified script copies the new stimtimes6.txt file into the stimuli directory (of a new subject folder) and uses it for the regu
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nic
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AFNI Message Board
Hi Rick,
Thank you for your answer!
I seem to have found a solution but don't quite understand why this works. Apparently, I need to source these scripts from within the proc script (i.e., the script generated by uber_subject.py):
source stats.REML_cmd (I also tried to chmod for this script from within the proc (without sourcing it) but this didn't help)
source ./@ss_review_ba
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nic
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AFNI Message Board
Hi AFNI gurus and enthusiasts,
I'm running into a few puzzling, related problems with uber_subject.py.
After filling out the fields in the GUI, I click on the upper left document icon, which sets up the familiar folder structure and creates "cmd.ap.subj" in the subj folder. However, clicking on the right upper document icon produces an error message: "cmd.ap.subj: No suc
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nic
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AFNI Message Board
Hi Simone,
The problem may lie in using " vs '. At least, that's the exact problem I had today :) I'm working on a MAC and had to change from using ' to ". Also, you are using both in your command.
-wsVars "Condition*Delay*Time" \
vs
-gltLabel 1 'Negative' -gltCode 1 'Condition : 1*Negative' \
Hoping this does the trick,
N
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nic
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AFNI Message Board
Dear AFNIers,
I would like to use a WM lesion map, derived from a FLAIR image with the Lesion Segmentation Toolbox (LST) in SPM, as a mask to extract values of interest from a functional scan. However, I'm having troubles getting the images aligned properly. The FLAIR has AIL orientation and the functional scan RAI orientation. The LST output is in TLRC space (but seems aligned to a MNI t
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nic
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AFNI Message Board
Hi Gang,
Thank you for your quick answer! I was under the wrong impression that -bsVars is only to be used if I have two groups or more.
### I followed your suggestion but got the following error:
** Error:
Failed at GLT No. 1! Make sure that the model or GLT specification syntax is correct.
### This was the cmd:
3dMVM -prefix $output_dir/mvm_time_age \
-mask $output_dir/so
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nic
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AFNI Message Board
Dear experts,
I'm trying to set up a model to examine whether Age might affect the BOLD signal (8 tent functions) over time and space (i.e., when and where is the BOLD signal associated with Age). This is within one group (N=30) currently and kind of following Gang's Example 3 at . However, I can't get it to work.
Here are two of my attempts:
3dMVM -prefix $output_dir/mvm_t
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nic
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AFNI Message Board
Dear AFNI community,
I have a map with Fisher's test statistics and would like to use FWE correction on it. The AFNI gui, however, takes t- and f-values as threshold but not so much Fisher's statistic. Is this the end?
Thank you!
Nic
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nic
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AFNI Message Board
Daniel, how unfortunate for the mischievous student but perhaps very entertaining for the others.
Rick, I looked at that board entry but didn't realize it may be relevant, thanks!
Generally great news, thank you both so much!
Nic
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nic
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AFNI Message Board
Dear AFNI users,
A couple of my participants have a wrap-around artefact in their functional scan and I'd like to determine whether or not the brain data are invalidated. Looking at the BOLD signal, stats-, stdev-, and snr-maps is helpful but I don't know if it is ok to use this info in some way.
Is there something like SPM's wrap operation in AFNI? In a prior post, Daniel s
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nic
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AFNI Message Board
Hi Gang,
I just saw your message, sorry!
Using 3dWilcoxon worked rather well, i.e., the results make sense (and I may feel inclined to say that they are beautiful) with respect to location and direction. Therefore, I believe the sporadic but extreme outliers were addressed while the results are robust to show the expected patterns.
Do you have more specific questions? I would gladly pro
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nic
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AFNI Message Board
Hi Gang,
Reading up on Wilcoxon and looking at the results in detail I'm having a pretty good idea of what they mean.
So far no follow-up questions.
Thanks for your help!
Nic
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nic
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AFNI Message Board
Hi Gang,
It's a within-subject design in two groups though here I'm only considering one group (group comparison soon, e.g. MannWhitney).
I ran 3dWilcoxon but I'm not sure how to interpret this test. My thoughts: 20 participants = 20 ranked pairs in a given voxel and if the pre/post beta median ranks significantly differ, then this voxel shows a group-level scaling effect. Is
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nic
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AFNI Message Board
Hi everyone,
I am dividing visual stimulation (task) betas by breath-hold betas (bh; 2 separate scans) to reduce cerebrovascular contributions to the task BOLD signal. Some of the bh betas are very low and so division results in "interestingly" large task betas. These greatly distort pre/post-scaling investigations.
Question: What are methods/decision rules to eliminate extreme va
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nic
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AFNI Message Board
Hi AFNI experts,
I would like to revive this thread because I couldn't find an answer on the message board except for this one.
Just like above, I am comparing two groups (20 controls vs 13 patients), including one covariate (age), using 3dMEMA. The output has t-stats for the between-group comparison as well as for the group that was entered first (patients as I'm interested i
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nic
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AFNI Message Board
Maybe I should add that the bh BOLD response is delayed by >10 sec and very sluggish, slowly coming back down so that I model far into the rest block. This choice was based on prior literature with which my data are in agreement.
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nic
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AFNI Message Board
Hi Rick,
Thanks again! The info on TENTzero was very helpful!
I had run the analysis using TENT(12.5,42.5,7), which looks very good. Another option I considered was TENT(10,45,8) but I don't think I'm really gaining anything (probably rather the opposite).
Things I may have not appropriately considered:
- There is not much of "rest" left
- There are 6 "stimuli
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nic
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AFNI Message Board
Hi Rick,
Thank you for your answer and resulting aha moments! Some follow-up questions:
“... applying a maximum censor number or fraction limit in a similar manner to BLOCK ... The key is just having enough (relatively independent) samples for each TENT beta.”
My current thoughts on exclusion decisions based on max censored TRs in a block design (using censor limit of 0.4 mm in afni_pro
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nic
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AFNI Message Board
Dear AFNI experts,
I'd like to use TENT functions to estimate the shape of the HRF for a breath-hold (bh) task. My goal is to use bh percent signal change (psc) to scale some task-related psc. Tents are new territory for me ... model specifications below.
Do you have any suggestions as to how many TRs/tent can be censored while still having valid results? TENT vs BLOCK produce the same
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nic
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AFNI Message Board
Hi Rick or anyone who may have a suggestion,
I have generated a 50x50 matrix and let it run over 50 time points (in MATLAB). The result is a 2500 x 50 matrix, each of the 2500 rows is a "voxel" with a time course of 50 points. It is only one slice, not a 3D volume, and I'd like to use my general preprocessing pipeline and try various group statistics on that slice once I have ge
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nic
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AFNI Message Board
Hi Thalia,
You could also choose "Dataset#N" in the Tran 1D step (instead of "Dataset#2") and go from there. This works for me anyways.
Nic
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nic
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AFNI Message Board
Hi everyone,
I am using 3ddelay to estimate the BOLD delay for blocks of breath holding (compared to rest).
The preprocessing pipeline follows these steps in order: time-shifting, volume registration, tlrc'ing, mean scaling, and detrending of the data (no spatial smoothing).
I did analyses with three different wave forms (square wave, a gamma variate, and waver; cmds below) as som
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nic
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AFNI Message Board
Hello Daniel, hello Gang,
We are updating AFNI and I'll refit my 3dmema output.
In general, I thought that I would probably not have to worry about these "holes" (just realized that this is a badly chosen word - it's just voxels missing a color input because of value "0"...just wanted to note that) because these are just very small beta and t-values that got t
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nic
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AFNI Message Board
On another note, why is it in ORIG template space?
Thank you as always so much!
Nic
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nic
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AFNI Message Board
Hello Gang, hello Rick,
Yes, these voxels are not assigned any color and have the value of "0".
Gang, here is the output:
$ 3dinfo -verb all_mema_reml_avsc_anti+tlrc.HEAD
++ 3dinfo: AFNI version=AFNI_2011_12_21_1014 (May 25 2012) [64-bit]
Dataset File: all_mema_reml_avsc_anti+tlrc
Identifier Code: XYZ_sMdO0E_C0CCOl3C9LEccSQ Creation Date: Tue Aug 21 17:41:24 2012
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nic
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AFNI Message Board
Hey Rick,
I'm having the same problem with 3dmema output. This is stored in short by default and it doesn't look like that there is an option to store in float (or default like 3dttest++), correct? None of the individual REML output (float) has these "holes" (which have a value of 0). I've been playing around with 3dcalc's -datum float on 3dmema output, masks, etc
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nic
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AFNI Message Board
hey rick,
i already included -giant_move. however, i then tried several alignment cost functions and -lpcZZ actually did a great job :) (aside from some others but lpc by itself was not successful)
thanks!
nic
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nic
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AFNI Message Board