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_afni -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/afniHQ/afni.build/pub.dist/bin/linux_ubuntu_24_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.
The script follows the following steps:
1- Strip skull off of ANAT+orig
Output is called nosk.ANAT+orig and is reused if present.
2- Transform nosk.ANAT+orig to TLRC space.
Output is called nosk.ANAT+tlrc and is reused if present.
3- Create ROI in TLRC space using 3dcalc.
Output is ROIt.PREFIX+tlrc and is overwritten if present.
4- Create ROI in GRID's orig space using 3dFractionize.
Output is ROI.PREFIX+orig and is overwritten if present.
Examples ( require AFNI_data3/afni, and
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
If you want another ROI given the same -anat and -base volumes:
@fast_roi -region CA_N27_ML::Superior_Temporal_Gyrus \
-region CA_N27_ML::Putamen \
-base TT_N27_r2+tlrc. -anat anat1+orig.HEAD \
-roi_grid epi_r1+orig -prefix toy -time
