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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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Oh! Sorry about that!
This is a regular EPI dataset. I just chose this colour scheme in the overlay, because I find it easier to see if anatomical markers (e.g. ventricles) are lining up with the underlay. But this a regular EPI with continuous intensity. The anat I enter into align_epi_anat is also skull-stripped (and the skull-stripping is good). I'm doing volume registration, skull-str
by
mrinmayi
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AFNI Message Board
Hello AFNI-gurus!
I'm aligning EPI to anat using align_epi_anat.py. Here is the command I'm using:
align_epi_anat.py -anat ${Part[${SLURM_ID}]}_T1_S+orig \
-epi ${Let}_${run}_Cat_S_TS_VR+orig. \
-volreg off \
-epi_base 0 \
-deoblique off \
by
mrinmayi
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AFNI Message Board
Hello AFNI gurus!
tl;dr: What is the best way to remove spikes in fMRI time series that occur as a result of using a clustered acquisition protocol?
We are running an auditory study using a clustered acquisition protocol. Each trial consists of a 10s scanner OFF period, followed by a 16s scanner ON period. The auditory stimulus that we will be modeling is presented 1500ms into the scanner OFF
by
mrinmayi
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AFNI Message Board
Hi Rick,
Thanks a lot for your response!
With regards to option 2, just to make sure I understand: does the inclusion of this factor in the baseline not make a difference because AFNI calculates the partial statistics of the Betas for the regressors? Such that the null hypothesis for EACH regressor contains this "error trials" regressor anyway?
If so, in what scenarios is the -st
by
mrinmayi
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AFNI Message Board
Hello,
I am using 3dDeconvolve with the -stim_base option to include trials with incorrect responses to the baseline (as suggested in another message board post).
I use the -stim_times format to define the rest of my regressors, but it seems that in order to use the -stim_base option I will have to make a -stim_files style file for the incorrect trials. Problem is, that my stimulus does not
by
mrinmayi
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AFNI Message Board