7.1.311. @fast_roiΒΆ

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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.

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

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