Not sure about #3, but the final white surface is created by the second call to mris_make_surfaces. That binary is called twice, the first time it creates the preaparc file
On 03/01/2017 09:41 AM, miracle ozzoude wrote: > Thanks Antonin. For 3) what does " min #of neighbors which must be on > to retain a point/specify fill_holes threshold" mean exactly? Also, I > noticed a difference in FS v5.3 and FS v6.0 ReconAllTable for creating > white matter surface. For v5.3, ?h.white is created as one of the > outputs for mris_make_surfaces while for v6.0 it has been replace with > ?h.white.preparc. At what stage is the final ?h.white surface created > for v6.0? > Best, > Paul > > On Tue, Feb 28, 2017 at 5:05 PM, Antonin Skoch <a...@ikem.cz > <mailto:a...@ikem.cz>> wrote: > > Dear Paul, > > 1) You find pretty thoroughful info on expert options file here: > https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#ExpertPreferences > <https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#ExpertPreferences> > > 2) recon-all -autorecon2-cp -autorecon3 is ok (btw -autorecon2-cp > and -autorecon2-wm runs the same commands, at least in version 6.0). > > 3) There is in the souce code following comment on -T option in > mri_fill: > min # of neighbors which must be on to retain a point > Default value is 1. > > Regards, > > Antonin > > > > Hello Freesurfer, > I have couple questions. > 1) If I have 2 commands (e.g., mri_normalize -a 30 and mris_inflate -n 30) > and I want recon-all to execute both commands. Should I create 2 different > expert opts files or 1 expert opts file with both commands in it? Also, > how > do I include the expert flag with recon? > 2) If I have added control points and wm edits to a subject, it is > accurate > to start from control points? i.e., recon-all -autorecon2-cp -autorecon3 > 3) Lastly, I am playing around with mri_fill command and I did like to > know > what -T flag does? > Thank you > Best, > Paul > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <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 > <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 mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
