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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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Thanks for your reply, Rick.
A couple of things not clear to me.
Regardless, the goal is to find a fit to the interaction
term, perhaps while ruling out a fit to just the seed.
Even if the seed happened to be a combination of task
regressors, we would not care (multicolliearity aside),
because those terms are all considered "noise" in the
model. Only the interaction result
by
bogadhiar
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AFNI Message Board
Hi,
I have a basic conceptual question regarding the context dependent correlation analysis.
In the context dependent correlation analysis as described on the afni page for CD cor Ana ,
it says to include interaction regressors and the seed regressor in the original regression analysis which has the task related regressors (independent variables) and regressors of no interest.
The questi
by
bogadhiar
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AFNI Message Board
I tried the censor option. It works fine. But, when I look at the fits with the data. I still see the the first two TRs in fits and they are the same as in data. So, I wasn't sure if the first TRs were modeled or just shown in the fits with the same value as in data. Can you clarify that?
by
bogadhiar
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AFNI Message Board
Hi,
Can anyone tell me a way to manage negative stim_times in 3ddeconvolve.
I throw away the first two 2TRs in each run but the stimulus started at the beginning of the run.
I get a warning saying unusable stim times.
Amar
by
bogadhiar
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AFNI Message Board
I figured out what was going worng when I compared the data to the fitt.
The first 2 TRs from each were included in the regression which was causing the problem.
Thanks again.
by
bogadhiar
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AFNI Message Board
I don't exactly understand your first suggestion,
When I use the wild card in 3dDeconvolve, Isn't each run modeled separately with its own set of regressors for that run?
If thats not the case, Using 3dDeconvolve Do I have to do the regression separately for each run?
by
bogadhiar
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AFNI Message Board
I was doing the analysis in MATLAB previously. I computed the t-statistic using BOLD values for Baseline condition Blocks Vs condition A Blocks for all runs across sessions. All the time series data in each run is expressed as percent of the mean (scaling) before the analysis.
Here is the 3dDeconvolve code I used for the regression: B0,FA0,PA0 are the baseline, FA, and PA blocks where monkey
by
bogadhiar
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AFNI Message Board
I tried with 10 runs from one session. Still I see the negative beta values but the no of voxels with negative beta values is alot lower than when I did the analysis across all runs i had.
Still, one thing not clear to me is when I just compute a t-score between baseline condition and motion present condition i get alot of voxels with positive t-scores especially in areas expected to respond to
by
bogadhiar
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AFNI Message Board
Hello afni users,
I was running analysis on my data set (125 runs across 8 sessions) in AFNI for the first time using 3ddeconvolve.
My experiment has 3 conditions in blocked design. Baseline: fixation task. A: fixation task with peripheral motion stimulus B:attend to motion. Some percent of the blocks from all three conditions where monkey's fixation has not met the criteria has to be ex
by
bogadhiar
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AFNI Message Board
One quick question,
for context-dependent correlation analysis
CD_CorrAna.html says to use option -stim_file in 3ddeconvolve which is the old method.
Is there a way to do the correlation analysis in the new recommended method using stim_times.
Thanks
by
bogadhiar
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AFNI Message Board
Thanks for the link.
One point is still not clear to me.
I see that the data time series (3d vol ts) is scaled before 3dDeconvolve and 3dTcat in the example program.
but it doesn't look to be detrended before concatenating across runs from different sessions.
For context-dependent correlation analysis (http://afni.nimh.nih.gov/sscc/gangc/CD-CorrAna.html),
The input data time serie
by
bogadhiar
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AFNI Message Board
Thanks for the suggestions.
I was reading one of the example scripts ('@DDmb_analyze '), and it suggests '3dTcat' to concatenate all the runs and the concatenated output of '3dTcat' be used as input to 3dDeconvolve. The questions I have is, Should I detrend each run before I concatenate all the runs from different sessions and use the concatenated file as input to
by
bogadhiar
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AFNI Message Board
Does the percent of 'blocks of no interest' compared to total blocks affect the analysis?
And, Can I concatenate all the runs across sessions and do the analysis instead of doing the analysis on each run separately.
Reason is, I might not have enough blocks on each run given the size of the 'blocks of no interest'.
Is there something I should be careful about when I con
by
bogadhiar
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AFNI Message Board
Hi,
I am thinking of doing a context dependent correlation analysis on my data set collected in a block design with three types of blocks.
Data set has multiple runs across multiple sessions. In each run, I have to select the blocks depending on monkeys behavior (e.g. eye movements). I want to run the context dependent correlation analysis on those selected blocks. How can I accomplish this?
by
bogadhiar
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AFNI Message Board
Hi,
I have collected few sessions of data where orientation of the monkey's head in the slice package is tilted towards its right.
I was thinking if I can use "3drotate" to rotate the EPI and FLASH volumes so that scans look symmetrical in the slice package.
Is it alright to use "3drotate" in this case without any issues affecting the further analysis of the data?
by
bogadhiar
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AFNI Message Board