Dear Freesurfer experts,

I am not an expert in manual edits, so I highly appreciate any feedback regarding the issues in my questions below. I ran the following command line “recon-all -s subjid -all” on T1 image for one of the subjects. when reviewing the output images (i.e. wm.mgz, brainmask.mgz) I found issues as attached.

Attached is an output of the command: "Freeveiw orig.mgz wmparc.mgz wm.mgz"

1.       When I reviewed “wm.mgz” I see interactions between the white matter (wm), and the cortex (yellow arrows). To fix this, I edited “wm.mgz” by removing the wm voxels from the cortex, and the data was saved in the file “wm.seg.mgz”

2.       I found many holes in many slices similar to the (black arrow). I filled all these holes. The data saved in “wm.seg.mgz”

3.       I fixed some issues related to dura and bad skullstipping

Then I ran the command: 

Now, I want to understand where Freesurfer implement the new edits? Which files will be used as the main files that include the new edits. Logically, the edits must be implemented in "wm.mgz" and "brainmask.mgz". What confuses me is when I open orig.mgz wm.mgz and brainmask.mgz in freesview. I see the original non-edited files. I am not sure what I am doing wrong so I highly appreciate any help.