Here are my analysis procedures:
3dDeconvolve -input catrunregblurob+orig -polort 2 \ catrunregblurob +orig is the Bold which has been tshifted,registered,blurred and deobliqued
-num_stimts 9 \
-stim_file 1 s_PULSE.1D -stim_label 1 "PULSE" -stim_maxlag 1 6 \ s_PULSE.1D, s_PPI.1D and s_PPI2.1D are the stimulus timing files
-stim_file 2 s_PPI.1D -stim_label 2 "PPI" -stim_maxlag 2 6 \
-stim_file 3 s_PPI2.1D -stim_label 3 "PPI2" -stim_maxlag 3 6 \
-stim_file 4 'motionrun[1]' -stim_label 4 "Roll" \ motionrun is from registration.
-stim_base 4 \
-stim_file 5 'motionrun[2]' -stim_label 5 "Pitch" \
-stim_base 5 \
-stim_file 6 'motionrun[3]' -stim_label 6 "Yaw" \
-stim_base 6 \
-stim_file 7 'motionrun[4]' -stim_label 7 "IS" \
-stim_base 7 \
-stim_file 8 'motionrun[5]' -stim_label 8 "RL" \
-stim_base 8 \
-stim_file 9 'motionrun[6]' -stim_label 9 "AP" \
-stim_base 9 \
-concat concat.1D \ concat.1D is gives onsets of the beginning of runs.
-iresp 1 Pulse.IRF \ *.IRF is the output of impulse response functions
-iresp 2 PPI.IRF \
-iresp 3 PPI2.IRF \
-mask maskrun+orig \ maskrun+orig is found by: 3dAutomask -prefix maskrun catrunregblurob+orig
-bucket Deconmotionrun \
-fout -tout -vout -rout -bout
The Volume+orig is deobliqued as follows: 3dWarp -deoblique -prefix Volumeob Volume+orig
Then the Volumeob+orig is converted to Talaraich space the old way using markers obtaining Volumeob+tlrc
Next we convert Deconmotionrun to +tlrc space by: adwarp -apar Volumeob+tlrc -force -dpar Deconmotionrun+orig -dxyz 2.0
PLEASE let me know what to change in the above analysis to allow us to use an old +tlrc Volume of the same subject at another date since we couldn't collect the Volume of the subject in this last scan. What are your suggestions?
Thanks!
-Linda
