Split an ROI mask into half and half along the anterior-posterior axis

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1

Hi AFNI masters,

Is there any way I can divided an ROI mask into half and half along y axis. This ROI mask was previously defined using cluster method in AFNI from functional localizer scans.

Thank you so much!

Zhen

2

Hi-

Well, you can use 3dcalc to specify conditions based on either i, j, k index coordinate values or x, y, z physical space coordinate values; see the 3dcalc help section: “COORDINATES and PREDEFINED VALUES” for more details.

In your case, you could use this to specify that you want to keep all voxel values for some y > YTHR and zero out the rest-- that seems to be what you are asking about. So, the syntax would be something like this:


3dcalc -a INPUT -expr "a*step(y-YTHR)" -prefix OUTPUT

… where you need to state what your YTHR value is; to get the other side of the ROI, you could calculate:


3dcalc -a INPUT -expr "a*not(step(y-YTHR))" -prefix OUTPUT2

If you wanted to get the “center” of your ROI in some sense along the y-axis, you could use 3dCM to get the center of mass location within a mask, and use the y-value there for YTHR.

–pt

3

Thank you so much! That’s extremely helpful! But I’m not familiar with 3dCM. I am reading the Output of -help. I think it should be something like this?

3dCM INPUT

Thank you!

4

Hi-

In order to use the coordinate values, you can dump them into a variable, then use that variable. In tcsh syntax this could be done:


# go into tcsh mode, if not there already
tcsh
# calculate the center of mass of the input data set;  if the ROI is smaller, then use "-mask ..." to select just the ROI of interest; store the (x, y, z) physical coordinates in the variable named xyz.
set xyz = `3dCM INPUT`
# print the y-value to the screen (just for fun)
echo $xyz[1]
# use the y-value as the boundary point above which to 'keep' showing the ROI of interest
3dcalc -a INPUT -expr "a*step(y-$xyz[1])" -prefix OUTPUT

–pt

5

Thank you so much!