Hello Bruce,
I think this ties to one of my previous questions. Most of the volumes I processed need both wm and pial edits (typically deleting incorrectly added voxels for both). More recently, I was editing wm.mgz for wm and brainmask.mgz for pial. From the wiki, if changes are made for both wm/pia, one can run recon-all -autorecon2 -autorecon3 and both changes would be incorporated, however with some volumes this does not happen: pial edits are incorporated correctly, but wm edits are not, I am not sure why, event though FS6.0.0 sees edits (running recon-all with -showedits points to edits in sm.mgz as well, and those edits propagate into filled.mgz. So next, I plan editing brain.finalsurfs.manedit.mgz for pia ( it turns out one cannot edit this also for wm when that means deleting voxels for wm), wm.mgz for wm, then run -autorecon2-wm -autorecon3. Is this a strategy, and if there are alternatives, please let me know. Also, for some reason, running recon with '-make all' does not seem to work.
Thank you,
Octavian
On Thu, Mar 30, 2017 at 8:51 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Manuel
-autorecon2-cp runs all the steps that autorecon2-wm does so it is redundant. If you run autorecon2-cp and autorecon3 you will get everything (unless you edit the aseg)
cheers Bruce On Thu, 30 Mar 2017, Manuel Delgado wrote:
Dear list, There is an issue that I have been concerned about since the beginning
of my
FS learning, as I have found somehow contradictory information in the tutorials. Is there a way to do an only recon-all after all the edits
have
been made to a subject? For example, if you have edited all the possible steps (skullstrip, control points, wm and pial surface) is it possible to use all the flags for each step in one only step? Something like: recon-all -autorecon2-cp -autorecon2-wm -autorecon-pial -autorecon3
-subjid
<subject>
Or on the other hand each step needs its own recon-all with its
appropriate
flag? Thank you
-- Manuel Delgado Alvarado, MD Neurology Department Neuroimaging Unit Valdecilla Biomedical Research Institute, IDIVAL Santander, SPAIN
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
-
Octavian Lie