Which volume are you re-creating? Changing the wm.mgz will not affect the aparc+aseg much (except through changes to the surface. The white surface may or may not change much, depending.
On 01/27/2017 03:33 PM, Gundel, Tristan J wrote:
Hello,
The link below will allow you to see the subject in question. It contains the anonymized verson of the original T1 image, as well as all of the corresponding masks and surfaces created with freesurfer. The particular area we are having issues with is located around (8.01, -45.57, 41.95). Any insight you could provide us about how to ensure that the aparc+aseg.mgz and wm.mgz correspond accordingly would be much appreciated. Thank you!
https://ucsf.box.com/s/cmsk4di0q4b5u7e3oxutp1d19ds314h4
Best Regards, Tristan
*From:* Gundel, Tristan J *Sent:* Tuesday, November 15, 2016 9:22 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Edits to White Matter
Hello,
I work in a lab that is currently using the Freesurfer algorithm to collect data from MRI images of individuals with Multiple Sclerosis. In order to increase the precision of our white matter masks we have combined your algorithm with ANTS, hoping to achieve more accurate surface volumes and aparc+aseg masks. Unfortunately we have had some issues when we edit our ANTS white matter mask (using value of 255) and then put it through freesurfer again, re-running recon-all (recon-all -autorecon2 -wm -autorecon3 -w <subID>). Our wm_surface and aparc+aseg mask do not change based on the edits we have made, and do not follow the white matter volume surface volume. How can we be sure that our white matter mask, and the edits we make to it, are considered in the creation of wm_surface and aparc+aseg mask? Please let me know if any of this is unclear and I will explain it in more detail.
Thank you, Tristan
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