Re: [Freesurfer] mri_watershed: really bad skull stripping
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: fis...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu 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: fis...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu 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 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 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 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.
Re: [Freesurfer] mri_watershed: really bad skull stripping
I'm glad to hear it improved. cheers Bruce On Sat, 30 Aug 2014, Úrsula Pérez Ramírez wrote: 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: fis...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu 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 fo r recon-all if I have already the .mgz file?, I'm getting errors, appart fro m the warning for updating tcsh. Cheers, Ursula Date: Fri, 29 Aug 2014 11:23:06 -0400 From: fis...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu 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 (al mo st nothing) with mri_watershed –atlas in images converted from DICOM to .mg z with mri_convert. I lowered the threshold but did not improved considera bl 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 Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The informati on 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 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 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] mri_watershed: really bad skull stripping
Hello, I’m new with FreeSurfer and I’m getting a really bad skull stripping (almost nothing) with mri_watershed –atlas in images converted from DICOM to .mgz with mri_convert. I lowered the threshold but did not improved considerably. I have tried with a subject from the tutorial dataset and it’s OK. What can be the problem? Thank you very much! Úrsula ___ Freesurfer mailing list 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.
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 (almost nothing) with mri_watershed –atlas in images converted from DICOM to .mgz with mri_convert. I lowered the threshold but did not improved considerably. I have tried with a subject from the tutorial dataset and it’s OK. What can be the problem? Thank you very much! Úrsula ___ Freesurfer mailing list 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.
Re: [Freesurfer] mri_watershed: really bad skull stripping
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: fis...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu 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 (almost nothing) with mri_watershed –atlas in images converted from DICOM to .mgz with mri_convert. I lowered the threshold but did not improved considerably. I have tried with a subject from the tutorial dataset and it’s OK. What can be the problem? Thank you very much! Úrsula ___ Freesurfer mailing list 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 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.
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: fis...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu 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 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 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.
