External Email - Use Caution

Hi,

I enjoy the output of synthstrip, thank you all for developing it. I am asking 2 questions to better understand how it interacts with FreeSurfer.

If you run the output of synthstrip on a T1.mgz in recon1 to create a better brainmask.mgz, there is no effects of synthstrip further downstream, because the brainmask is in of itself a mask only, and the nu.mgz, which was untouched by synthstrip is used to create the brain.mgz and etc. So the intensity normalization that is done within synthstrip does not determine anything downstream.

Using the brainmask.mgz for visual quality check after recon-all finishes only creates an illusion that this much better branimask was used to create the aparc+aseg.mgz/pial/white lines etc.
So for example, say I have a nu.mgz/T1.mgz that has a motion artifact and synthstrip fixes it. Yet recon2/3 is running the aparc+aseg.mgz on the unfixed nu.mgz/T1.mgz. Likewise, hippocampal subfield is run on the unfixed nu.mgz/T1.mgz

If I wanted to apply the intensity normalization procedures that synthstrip.mgz uses, I would use it to overwrite the T1.mgz. However it is unwise to have a skull-stripped image such as the output of synthstrip be put in that stage.

Is this all correct

2) Considering that I am correct for q1, if you are manual editing the brain, using the post-synthstrip brainmask.mgz and T1.mgz as the reference, you are in fact drawing back pre-synthstrip voxels into the brain. But it doesn't matter you're mixing pre or post-synthstrip voxels because brainmask.mgz is only used as a binary mask. Is this correct?

Victor Zeng

Beth Israel Deaconess Medical Center

Vial of Victory LLC

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