External Email - Use Caution
Hello all,
?
There are two topics I would appreciate your expert advice on:
Topic 1: Aseg and wm edits
I was going through the wiki and the archive of past inquiries and was unable to find a clear answer to whether you can make aseg edits and wm edits, and then re-run in Freesurfer at the same time. Furthermore, I was just a little unclear as to how exactly to perform aseg edits.
According to this post:
https://secure-web.cisco.com/1RxWuWDKVwztKCLSwXj6z1drGBPyh2kvn_19UWiYuyqKvR-...,https://secure-web.cisco.com/1RxWuWDKVwztKCLSwXj6z1drGBPyh2kvn_19UWiYuyqKvR-6gfAr-hoqMyohobauYuBxjBP3YqZOy59M2NF3uc09-AWtpXiG4yYKE2CTKAkxSa89FX24-NeKmVdVYrpgl9G2Hp80p128PEGO_3fbZmz1utpMLRUM4VSnFr4IeKIl_5zBo9K7XkcqCHWKCGm3vwj2r8UHoj9tSnmgcdSP-m0zwmpCdiufHYb8zVZHHuj3gLXtgzmNWNgD3AhyYasPZvLU5p1nKNIuMGwuTz9RAMQ/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg67321.html you are supposed to edit aseg.manedit.mgz, and only make edits to wm.mgz if segmentation is still incorrect after re-running. The command suggested to be used is recon-all -s subject -autorecon2 -nogcareg -nocanorm -nocareg -autorecon3.
However, according to this post:
https://secure-web.cisco.com/12Lq8z3kDRX5hmVV3-U_tQM9lMGELV_rZuE0w7MEaZ6-3fA... and the wiki page it references here:
https://secure-web.cisco.com/1Ktb4SEXIjUqckJnfQRhLq0dVZmG77-DlcegK4GTCJhXvPo...,https://secure-web.cisco.com/1Ktb4SEXIjUqckJnfQRhLq0dVZmG77-DlcegK4GTCJhXvPo4192P7mmvIsYZP0mCPZp1d9q3-KWGQgZr0kjE5DljVI3SCoWb5zyRilBaQ14RYilG07LVOwCnTWeBvNDkuspktUi3yFxkEZ8mgyQAAAUdBeCyJfgddc2uNKpw9UbPp9L2xQTsZ2_ZccOLN6YzjPTVc_fdIGEGQuJ-P_JY6w4PfZ3YnPgHfyk4_HqVx4XKzIP4PP97GcfBzJGbbPqCMyeHzHJT7KqOBYN31IzdVkg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FTkMeditGuide%2FTkMeditWorkingWithData%2FFreeviewSegmentations you are supposed to edit aseg.presurf.mgz, and doesn't mention whether aseg edits are compatible with wm.mgz edits. The command these posts say you should run is recon-all -autorecon2-noaseg -autorecon3 -s subject, and this is also listed in the "OtherUsefulFlags" table.
My questions are:
1) Does it matter which volume, aseg.presurf.mgz or aseg.manedit.mgz that you edit?
2) What is the proper command to use for re-running with aseg edits?
3) Can you make edits to wm.mgz and aseg edits and re-run with both edits being taken into account?
For some background into why I've been looking into editing aseg segmentations, we have a sizeable portion of our data for whom the lateral ventricles are being mislabeled as wm (for some this is quite mild, for others it is pretty extensive). I know the -big-ventricles flag is an option, but we are not looking to re-run all of our subject with it at this time, as we have 100+ subjects.
Topic 2: White/pial overlap near subcortical structures
Sometimes, the pial surface near the subcortical structures will "pull back" too much, I've attached an example image. This "pull back" sometimes appears after I've re-run the subject after making wm edits, when it was not present in before re-running. In the attached example image, the original pial surface before re-running is in blue, the new pial surface is in red. The original white surface is in green, the new white surface is in yellow. I have the aparc+aseg.mgz and wm.mgz visible. As shown in the image, this "pull back" will often end up exclude a chunk of voxels from the aseg and aparc+aseg, even if there are wm.mgz voxels filled in that area.
How important is it to fix errors in this area in general, and would aseg edits be appropriate since wm edits don't seem to address the problem?
Thank you for your insight into these topics!
Sincerely,
Jee Won
