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.