Hi all, Thanks Bruce for your recommendation, with recon-all I obtain a much better skull stripping. Now I'm going to change thresholds because at the top and bottom slices the segmentation is inadequate: central segmentation is missing. Cheers, Úrsula
Date: Fri, 29 Aug 2014 11:48:51 -0400 From: [email protected] To: [email protected] Subject: Re: [Freesurfer] mri_watershed: really bad skull stripping you can give any format we support to recon-all as the input, including .mgz cheers Bruce On Fri, 29 Aug 2014, Úrsula Pérez Ramírez wrote: > Hi Bruce, > > thank you very much for your fast answer. I'm running outside recon-all, > only with mri_watershed. Thanks, that could help. Which are the options for > recon-all if I have already the .mgz file?, I'm getting errors, appart from > the warning for updating tcsh. > > Cheers, > Ursula > > Date: Fri, 29 Aug 2014 11:23:06 -0400 > From: [email protected] > To: [email protected] > Subject: Re: [Freesurfer] mri_watershed: really bad skull stripping > > Hi Arsula > > are you running this through recon-all or outside of it? The skull > stripping works better after the intensity normalization that is part of > recon-all > > cheers > Bruce > > > On Fri, 29 Aug 2014, Úrsula Pérez Ramírez wrote: > > > > > Hello, > > > > > > I’m new with FreeSurfer and I’m getting a really bad skull stripping (almo > st > > nothing) with mri_watershed –atlas in images converted from DICOM to .mgz > > with mri_convert. I lowered the threshold but did not improved considerabl > y. > > I have tried with a subject from the tutorial dataset and it’s OK. What ca > n > > be the problem? > > > > Thank you very much! > > > > > > Úrsula > > > > > > > > _______________________________________________ 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. > > _______________________________________________ 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.
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