Hi Fereshte,
I ran a few tests- mri_watershed will likely fail on volumes that are not intensity normalized (001.mgz, rawavg.mgz, orig.mgz). It should work on any other volume. Emma ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Fereshte <fereshte.ramez...@gmail.com> Sent: Friday, October 27, 2017 2:40:09 PM To: Freesurfer support list Subject: Re: [Freesurfer] Extracting labels using mri_watershed Hi Dear Emma, Here's the command : "mri_watershed -LABEL 001.mgz out.mgz" and the output file is attached. Thank you in advance Fereshte On Mon, Oct 16, 2017 at 6:45 PM Boyd, Emma <ebo...@mgh.harvard.edu<mailto:ebo...@mgh.harvard.edu>> wrote: Interesting.. would you mind sending me the command you ran and file drop the input and output volumes to me?: https://gate.nmr.mgh.harvard.edu/filedrop2/ Emma ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Fereshte <fereshte.ramez...@gmail.com<mailto:fereshte.ramez...@gmail.com>> Sent: Sunday, October 15, 2017 6:43:08 AM To: Freesurfer support list Subject: Re: [Freesurfer] Extracting labels using mri_watershed Hi Emma, I've tried this before but surprisingly not such labels in the output volume. On Wed, Oct 11, 2017 at 9:03 PM Boyd, Emma <ebo...@mgh.harvard.edu<mailto:ebo...@mgh.harvard.edu>> wrote: Hi Fereshte, mri_watershed -LABEL inputvolume.mgz outputvolume.mgz The output volume will contain 6 labels: 0 = exterior 1 = scalp 2 = skull 3 = csf 4 = gray 5 = white 6 = fat tissue Emma > On Oct 11, 2017, at 3:38 AM, Fereshte > <fereshte.ramez...@gmail.com<mailto:fereshte.ramez...@gmail.com>> wrote: > > Dear Experts, > How is it possible to extract labels like scalp and skull using -LABEL flag > in mri_watershed ? > Thanks for your attention. > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto: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 mailing list Freesurfer@nmr.mgh.harvard.edu<mailto: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.
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