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 [email protected] 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.
