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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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Hello AFNI experts, I non-linearly warped my functional data to the MNI152_T1_2009c+tlrc.HEAD template during preprocessing. In the AFNI GUI, I changed the coordinate system to LPI-SPM and I changed the brain displays to LR mirror. Are the coordinates that I see in the AFNI GUI and the clusterize report tables that I generate in MNI space or Talairach space?
by
emarler
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AFNI Message Board
Hello AFNI experts, I'm running 3dFWHMx to receive cluster thresholds for 3dClustSim and I'm wondering whether it more appropriate to use 3dREMLfit's -Rwherr files or 3dREMLfit's -Rerrts files? I am using the acf values from 3dFWHMx as the input for 3dClustSim to calculate cluster size thresholds for multiple comparisons corrections in 3dMVM. I ran 3dMVM using 3dREMLfit stats.
by
emarler
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AFNI Message Board
Hello AFNI experts,
I have been doing research on using 3dDeconvolve vs. 3dREMLfit, and it seems like 3dREMLfit is the ideal option because fMRI time series are temporally autocorrelated, and 3dREMLfit will attempt to account for this autocorrelation. It also sounds like 3dREMLfit will soon become the new default in first level analysis. Therefore, I would like to use 3dREMLfit stats when I ru
by
emarler
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AFNI Message Board
Hi Gang,
I was wondering if we could come back to this post because I also tried using -wsE2 in my 3dMVM script and got the same error. However, I was able to use the flag -wsMVT fine. How come -wsE2 doesn't work, but -wsMVT does? Also, to clarify, is -wsE2 a hybrid model that uses both univariate and multivariate analysis and picks the best method to apply to a certain brain region?
by
emarler
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AFNI Message Board
Hi Gang, thank you for the reply. I have run 3dMVM both with -SC and without. For some more information on my study, it is an event-related design and I am analyzing it using CSPLIN to estimate the BOLD response. My within-subject variable is time, of which there are 11 total timepoints. When I look at the cluster table generated by the output from -SC and without -SC, I see fewer clusters that s
by
emarler
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AFNI Message Board
Hello AFNI experts, I'm trying to decide whether I need to run a sphericity correction (using the -SC flag) on my data in 3dMVM, but I would like to know whether it is necessary by first seeing what the p-values are for Mauchly's test. According to a recent publication by Chen, Adleman, Saad, Leibenluft, and Cox (2014), the Mauchly test for sphericity correction can be readily incorpora
by
emarler
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AFNI Message Board
Hello,
I ran 3dDeconvolve on a CSPLIN model with the values (0, 22, 11) and a TR of 2.2 for an event-related design. When I pull up the results to check the activation maps, I have 11 timepoints to choose from. I'm wondering which of those timepoints I should choose to model in 3dttest++. For instance, does it make sense to use the average activity for each of the two tasks and/or the peak
by
emarler
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AFNI Message Board
Hello, I am trying to remove the last 10 TRs in one of 6 runs and I keep receiving an error when I use the command -tcat_remove_last_trs 0 0 0 10 0 0\ to do so. The error says this: ** error: option -tshifts_opts_ts follows unknown arg #34 (10). Is there another way to remove only the last few TRs for one run during preprocessing? Below is my preprocessing script.
afni_proc.py -subj_id DASHH_
by
emarler
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AFNI Message Board