This may be an "old school" approach, but here goes... Since you have warped to tlrc in your pipeline you can use the TT_N27+tlrc template (the default for afni_proc.py) to construct a mask.
1. Copy the file from your afni folder:
3dcopy ~/abin/TT_N27+tlrc ~/Desktop/your_files/TT_N27+tlrc
2. Create a mask from that template:
3dAutomask -prefix TT_Mask TT_N27+tlrc
3. Modify the resolution of your mask
3dresample -master SingleSubjectStatsFile+tlrc -inset TT_Mask -prefix TT_Mask_lowres
4a. Use your mask in your 3dttest++/3dMEMA command (modified from the help command)
gen_group_command.py -command 3dttest++ \
-write_script cmd.tt++.3 \
-prefix tt++.3_V-A \
-dsets stats*.HEAD \
-set_labels Vrel Arel \
-subs_betas 'Vrel#0_Coef' 'Arel#0_Coef' \
-options \
-mask TT_Mask_lowres+tlrc
4b. Use 3dcalc to mask your data that is already processed (will wipe out your stats thresholds and FDR)
3dcalc -a groupAnalysis+tlrc -b TT_Mask_lowres+tlrc -prefix forDisplayPurposes -expr 'a*b'
Edited 1 time(s). Last edit at 07/19/2012 12:24PM by Peter Molfese.
