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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 MH, I don't come here often, so sorry for the delayed response.
RetroTS is more fancy and handles RVT too, so it likely has the edge in effectiveness, and as Rick mentioned it's a popular option particularly for resting state fMRI by the sounds of it. However, I still use 3dretroicor often because it's easier for me to use in some cases, although I primarily do relatively str
by
Fred
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AFNI Message Board
3dretroicor wants cardiac pulse waveform data in a format like a "stim_file" input to 3dDeconvolve (i.e. something plottable with 1dplot). Fortunately, your list of R-wave times is like a "stim_times" input to 3dDeconvolve, and there just happens to be a tool for converting a stim_times data file to a stim_file format: timing_tool.py, e.g.
timing_tool.py -timing rwave.times
by
Fred
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AFNI Message Board
That's a longstanding issue: align_epi_anat.py doesn't like NIfTI files (it can't deal with the .nii or .nii.gz file names, only +???.HEAD/BRIK file names).
As Daniel mentioned, a workaround is to use 3dcopy to convert the files into AFNI file format.
by
Fred
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AFNI Message Board
Hi Daniel. In my experience, the effect is often small, but it varies from person to person. Usually, the standard deviation goes down slightly (look in the graph window) and a few obvious false positive voxels go away (though maybe not as much as I'd like), despite there being not much change in the power spectrum in the subjects I checked long ago. You can subtract the before and after dat
by
Fred
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AFNI Message Board
One column of raw voltage values is probably okay, and sampling rate doesn't matter as long as it's high enough and fairly constant. As Rick pointed out, if your EPI data are, for example, 200 s long then your physio data should be 200 s long as well, and in temporal alignment.
You don't need to do any peak detection beforehand as 3dretroicor has a peak detector for pulse data b
by
Fred
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AFNI Message Board
You may be better off rerunning the analysis using the TENT basis, as Rick suggested.
However, if averages are all you want, the ancient afni plugin "SingleTrial Avg" can do it without resorting to a lot of scripting. I have not used it in ages, but someone asked me about it last week, coincidentally. You need to create a .1D text file with a column of numbers, 0 for "off"
by
Fred
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AFNI Message Board