AFNI Message Board

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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March 16, 2017 10:37AM
Dear AFNI Experts,
We’ve performed a first level fmri analysis for 48 subjects by means of the 3dDeconvolve command as following:

3dDeconvolve \
-input ${tfMRI_input} -num_stimts 3 \
-stim_times 1 ${EVsFold}/cue.1D 'SIN(0,20,10)' -stim_label 1 ${fMRIName}_cue \
-stim_times 2 ${EVsFold}/math.1D 'SIN(0,20,10)' -stim_label 2 ${fMRIName}_math \
-stim_times 3 ${EVsFold}/qmath.1D 'SIN(0,20,10)' -stim_label 3
-polort 1 -fout -tout -bucket ${OutputF1}/${fMRIName}_stats_SIN.nii.gz \
-fitts ${OutputF1}/${fMRIName}_fitt_SIN.nii.gz \
-iresp 1 ${OutputF1}/${fMRIName}_pos_iresp_SIN_cue.nii \
-iresp 2 ${OutputF1}/${fMRIName}_pos_iresp_SIN_math.nii \
-iresp 3 ${OutputF1}/${fMRIName}_pos_iresp_SIN_qmath.nii

Thus obtaining in the output bucket: Full_Fstat, _Tstat, _Coeff and _Fstat for each stim_lab.
We’d like to perform a second level group analysis using 3dttest. Which of the contents of the bucket we have to use? Which sub-brick of the statistical bucket dataset contains the contrast file for the t statistic and f statistic (thus for F the extra sum of squares)? Do we have to produce additional output using -gltsym?
Subject Author Posted

Second level analysis from 3dDeconvolve output

fabio_mangini March 16, 2017 10:37AM

Re: Second level analysis from 3dDeconvolve output

gang March 16, 2017 11:47AM

Re: Second level analysis from 3dDeconvolve output

fabio_mangini March 17, 2017 05:25AM

Re: Second level analysis from 3dDeconvolve output

fabio_mangini March 17, 2017 07:23AM

Re: Second level analysis from 3dDeconvolve output

gang March 17, 2017 03:58PM