Usage: @fast_roi <-region REGION1> [<-region REGION2> ...]
<-base TLRC_BASE> <-anat ANAT>
<-roi_grid GRID >
<-prefix PREFIX >
[-time] [-twopass] [-help]
Creates Atlas-based ROI masked in ANAT’s original space. The script is meant to work rapidly for realtime fmri applications Parameters:
-region REGION: Symbolic atlas-based region name.
See whereami -help for details.You can use repeated instances of this option to specify a mask of numerous regions. Each region is assigned a power of 2 integer in the output mask
- -drawn_roi ROI+tlrc: A user drawn ROI in standard (tlrc) space.
- This ROI gets added with the REGION roi.
- -anat ANAT: Anat is the volume to be put in std space. It does not
- need to be a T1 weighted volume but you need to choose a similarly weighted TLRC_BASE. If ANAT is already in TLRC space then there is no need for -base option below.
- -anat_ns ANAT: Same as above, but it indicates that the skull
- has been removed already.
- -base TLRC_BASE: Name of reference TLRC volume. See @auto_tlrc
for more details on this option. Note that for the purposes of speeding up the process, you might want to create a lower resolution version of the templates in the AFNI. In the example shown below, TT_N27_r2+tlrc was created with:
- 3dresample -dxyz 2 2 2 -rmode Li -prefix ./TT_N27_r2
-input /home/ptaylor/afni_src/linux_ubuntu_12_64/TT_N27+tlrc.where TT_N27+tlrc is usually in the directory under which afni resides.
-roi_grid GRID: The volume that defines the final ROI’s grid. -prefix PREFIX: PREFIX is used to tag the names the ROIs output. -time: A flag to make the script output elapsed time reports.
- -twopass\ : Make TLRC transformation more robust. Use it if TLRC
- transform step fails.
-help: Output this message.
The ROI of interest is in a volume called ROI.PREFIX+orig.
3dresample’s output from command shown above):
- @fast_roi -region CA_N27_ML::Hip -region CA_N27_ML::Amygda
- -base TT_N27_r2+tlrc. -anat anat1+orig.HEAD -roi_grid epi_r1+orig -prefix toy -time