Hi Ben

we don't write out the mid saggital plane image, although we do compute it internally. mri_cc prints the transformation matrix, which you could paste into a .lta file and apply that transform to the data I guess.

Actually, looking at the code there is an old diagnostic you can use. Do

setenv DIAG 0x04048 setenv DIAG_VERBOSE 1

then run mri_cc (you can copy the command line from the recon-all.log or recon-all.cmd) and it should write a file named test.lta that you can use.

good luck Bruce

On Mon, 5 Mar 2018, Benjamin Yeske wrote:

Hello Freesurfer Experts, I am using freesurfer looking to get the cross-sectional area of the corpus callosum using the midline plane. Could you please explain how to define the midline plane in freesurfer so we can compute our cross-sectional area?

Thank you, Ben