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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 Daniel,
Thank you for telling me how to use that Freesurfer program correctly. Your suggestions addressed our issue in a simple way without having to do a conversion on my own.
Best,
Christine
by
Christine Smith
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AFNI Message Board
Hi Daniel,
It is a freesurfer program called mri_surfclust that is doing this. It outputs the Brainnetome regions, but the x, y, z coordinates of the peak statistical value is outputted as talairach coordinates. All the subjects for this analysis were aligned to fsaverage. Not sure if this was the issue. There is so little documentation/support for these freesurfer programs we are just trying
by
Christine Smith
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AFNI Message Board
Daniel,
I have an issue similar to this old post. I am analyzing my data in afni using the MNI152 template. I want to report freesurfer cluster locations in the same publications, but that program is outputting Talairach coordinates for the clusters.
Any suggestions on converting those Talairach coordinates into MNI152 coordinates?
Regards,
Christine
by
Christine Smith
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AFNI Message Board
Hi PT,
I am working with Catherine and can provide you with the information you requested to expedite this query.
Here is the output of each command:
# A
afni -ver
Precompiled binary linux_ubuntu_16_64: Mar 24 2021 (Version AFNI_21.0.21 'Titus')
# B
@FindAfniDsetPath TTatlas+tlrc
/usr/local/afni/bin
# C
afni -no_detach -q -VAFNI_GLOBAL_SESSION=
this command did no
by
Christine Smith
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AFNI Message Board
Hello,
We are trying to view the Brainnetome atlas in SUMA and we are having difficulty.
We downloaded the Brainnetome atlas file from the afni website (BN_Atlas_246_1mm.ni.gz), but it is unclear how to view that in SUMA and we also don't know what anatomy (underlay) to use to view that file in SUMA. We tried to view it on the fasverage brain and also an MNI_152 brain, but they did n
by
Christine Smith
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AFNI Message Board
Hello,
Is there a ttest-like program that can take into account how many trials (or how few!) one has for each condition of interest?
Regards,
Christine
by
Christine Smith
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AFNI Message Board
Thank you! I think the 3dmean program is what I was looking for.
by
Christine Smith
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AFNI Message Board
Hello,
Which program should I use to compute a voxel by voxel standard deviation across subjects?
I have a DTI measure similar to FA and I would like to see the mean and standard deviation (across participants) for this measure for all voxels in the brain.
Thanks,
Christine
by
Christine Smith
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AFNI Message Board
Hello,
Is there a way to evaluate a random stimulus timing file for 3dDeconvolve analysis in AFNI that was generated by a different program?
Our behavioral test can generate many stimulus timing orders that conform to the restrictions of the behavioral paradigm. Is there a way for us to import these vectors into AFNI and have it analyze them to find the ones that are most suitable for 3dDe
by
Christine Smith
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AFNI Message Board
Hello,
We are using afni_proc's volreg to align data to MIN_OUTLIER. We do not want to remove the first two time points of each run with 3dTcat. At the same time, we want the 3dToutcount to ignore the first 2 time points in its calculations. Is there an option in afni_proc that would let us ignore the first 2 time points in 3dToutcount. As it stands, we generate the afni_proc code and mod
by
Christine Smith
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AFNI Message Board
Hi Rick,
I can't seem to figure out how to get the reconstructed output file from Dimon to be written into the folder specified in 'gert_outdir'.
Here is my script:
Dimon -infile_prefix SS22_Structural/e177/s1547/i \
-gert_create_dataset \
-gert_outdir SS22_Structural/Flair \
-gert_to3d_prefix Flair.nii.gz
I run this script in a parent directory (Structural_Scans) t
by
Christine Smith
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AFNI Message Board
Perfect solution!
I'm off to the races now.
Thanks,
Christine
by
Christine Smith
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AFNI Message Board
Hello,
I am interested in creating an event list based in the 1D files that were created from make_random_timing.py.
What I am after is a list that simply tells me the order of the conditions. I imagine it would look something like this:
start of run1 start of run2
condition1 condition8
condition2 condition4
condition7 condition2
... ...
condition
by
Christine Smith
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AFNI Message Board
Hi Rick,
You mentioned that I "Currently you have 150s of rest, distributed in 3s
multiples (so 0 or 3 or 6, etc). Is that really how
you want it? Would you prefer a range, maybe 2..10,
say? It looks like the mean ISI should be about 5s,
the way you have set it up. "
For my experiment, I do not have true rest. Instead, I have an baseline 'task' that takes 3-sec to co
by
Christine Smith
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AFNI Message Board
Hi Rick,
Thanks for the reminder to bump up forgotten posts. I always thought that failures to respond meant you all were not willing to continue working on things. It is good to know that is not the case.
For my code, I added your suggestion of -rand_post_stim_rest no. I pasted in the relevant parts of the code below in the section titled "THIS IS THE make_stim_times code:".
by
Christine Smith
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AFNI Message Board
Hi Rick,
Wouldn't "post_rest 9" give me the 9 seconds (i.e. 3 baseline trials) I need at the end of each run?
You had asked about what the GLT would look like for "all the conditions together vs baseline".
When trying to create these GLTs I got confused because I will need to code the baseline conditions as 'rest' as far as 3dDeconvolve in concerned, t
by
Christine Smith
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AFNI Message Board
Hi Rick,
I get a weird error when I try to run your make_stim_times.txt program (see below) that has all the variables and scripting and the make_random_timing.py call.
The error says: set Variable name must begin with a letter.
In your code all the set commands are following by variable names that begin with a letter so I am thinking that something else must be going on.
Can you
by
Christine Smith
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AFNI Message Board
Hi Rick,
I like your idea of pretending that the active baseline condition is just another type of stimulus condition.
How would the program know that this extra task is also part of the same condition as the "-post_stim_rest" TRs? Or is there a way to force each run to end with 9 seconds of my baseline 'condition' and set "-post_stim_rest" equal to zero?
F
by
Christine Smith
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AFNI Message Board
Hello,
I am using make_random_timing.py for the first time and can't figure out how to get it work with an 'active' baseline instead of a 'passive' baseline, such as rest.
Specifically, I have people do an odd/even digit judgment task as my baseline. I am allowing them 3 seconds to do the judgment. Thus, my baseline trials have a minimum duration of 3 seconds and
by
Christine Smith
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AFNI Message Board
Gang,
I also wanted to mention that two of my participants do not have accuracy data, so I am reluctant to analyze correct and incorrect trials separately because I will not be able to include them in the analysis.
So, would it be best to handle the continuous nuisance variables (confidence and response time) at the trial level using amplitude modulated regressors and then handle the bina
by
Christine Smith
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AFNI Message Board
Hi Gang,
Because accuracy is one of these nuisance covariates, I would like to interpret the brain activity associated with the 4 time periods without the confound of accuracy. That is, accuracy decreases across the four conditions of interest (Time1, Time2, Time3, and Time4). However, I want to detect brain activity that changes with TIme, where the changes do not simply reflect the concomit
by
Christine Smith
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AFNI Message Board
Gotcha!
Gang,
One more point for one of the covariates. The covariate called Accuracy is actually a binary number when considering the trial data: 1 = correct and 0 = incorrect. In that case, would you proceed the same way to subtract the group mean for each condition of interest (i.e. Time1, Time2, Time3, and Time4)? For example, if the average accuracy for Time 1 across all participants
by
Christine Smith
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AFNI Message Board
Hello,
I am having difficulty deciding the best way to control for covariates in my analysis in my within-subject experiment. I want to identify the effects of Time on brain activity and control for some covariates. I have four conditions of interest (Time1, Time2, Time3, and Time4) and three nuisance covariates (Confidence, Response Time, and Accuracy). The covariates change as a function of
by
Christine Smith
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AFNI Message Board
Hello,
I would like some help deciding which multivariate analysis program to use for my repeated measures experiment: 3dLME vs 3dMVM.
My independent variable is Time. It has 4 levels and it is a repeated measure. I also have 3 nuisance behavioral measures that I would like to covary out of the analysis of the effect of Time. These three measures also change with the passage of Time (e.g.,
by
Christine Smith
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AFNI Message Board
Hello,
I have carried out an amplitude modulation analysis where I am asking which voxels are have BOLD amplitudes modulated by variable A and/or variable B or are unmodulated by these variables. So my -stim_times_AM2 input file looks like this: 20*15,30 44*2,10, etc.
For my output I get a beta coefficient and t statistic for the effects of interest: 1) unmodulated effect,2) the effect th
by
Christine Smith
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AFNI Message Board
Hello,
I am carrying out an amplitude modulated analysis for one trial type and want to know what to do with the other trial type in my 3dDeconvolve call (see below).
Is it correct to simply use the -stim_times option to code for this stimulus-of-no-interest so that it will not be considered part of the baseline? In the file (below) this is the 'Facts' condition.
My second que
by
Christine Smith
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AFNI Message Board
Hi Rick,
I work with marina. We definitely haven't updated Afni after may18th. We are using the manual that we downloaded off the Afni website about three weeks ago.
It sounds like this problem and the other issue we are having with aligning free surfer segmentations to Afni anatomicals (see marinas post above and Peters response) might be related to our outdated version of Afni.
by
Christine Smith
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AFNI Message Board
Apologies. My question was answered by an earlier thread titled "3dFWHM and AlphaSim".
Funny that my search for the phrase "3dFWHM and AlphaSim" did not bring up this earlier post from 08/2012. I forgot to use the Advanced Search option to search for older threads.
Regards,
Christine
by
Christine Smith
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AFNI Message Board
Page 1 of 3
Pages: 123