Hi Bruce and others, Thanks for the reply! I cloned in all of the brain to the brainmask and ran -autorecon2. What I have so far looks a lot better, but -autorecon2 exited with errors. In recon-all.log it looks like mris_curvature_stats went fine, then it says "INFO: mri_segstats will not calculate Supratentorial due to missing ribbon.mgz file"
I thought ribbon.mgz would be created in -autorecon3. Is it okay to just run -autorecon3 now, or should I fix something first? Thank you! Sara On 08/11/2014 11:54 AM, Bruce Fischl wrote: > It looks more likely that it is a problem with the skull stripping. If you > clone the brain voxels back in and rerun do things work? > >> On Aug 11, 2014, at 4:11 PM, "Makaretz, Sara Johanna" >> <[email protected]> wrote: >> >> I am having trouble getting a usable brainmask for one of my subjects - >> a screenshot of the initial brainmask.mgz is attached as image_1. The >> talairach transformation looks fine, so I tried running recon-all >> -multistrip with raised watershed heights to no avail - see image_2. >> >> Does this mean the problem is with the mri_em_register step / lta >> output? How can I check this, and what can I try changing? >> >> Thank you! >> <image_1.jpg> >> <image_2.jpg> >> _______________________________________________ >> Freesurfer mailing list >> [email protected] >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ 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.
