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?
