Masking Errors with 3dcalc

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1

Hello,

I am attempting to manually skull strip T1 and T2 images from a pig by creating a mask of the brain and using 3dcalc to multiply the dataset my the mask with values of 1 and 0.
I have done this hundreds of times in graduate school, and have never had issues using Linux Ubuntu. I am now trying to do this on a Mac.
The output files show some slices as expected, but some slices appear identical to the mask (ie the brain area has a value of 1 as opposed to the values from the data).

Has anyone experienced this or have any suggestions that I can try?

I have made sure my shell is in tcsh as opposed to zsh, I have reinstalled afni and gone through the "preparing for bootcamp" instructions. I used the same T2 file used to create the mask to make sure it's not a resampling issue.

AFNI version info (afni -ver): AFNI_24.1.04

2

Can you please post your 3dcalc command?

I dalso don't see why the shell should matter to 3dcalc, so that should not be an issue (as long as the variables and syntaxes are appropriate for the shell provided).

You can verify that your input datasets are on the same grid with:

3dinfo -same_all_grid -prefix DSET1 DSET2

... which should output five 1s if the five checked properties are the same. (Though I would expect 3dcalc to complain if they weren't.)

--pt