Re: [Freesurfer] mprage flag in recon-all
Hi Caspar it changes some parameters to the intensity normalization and segmentation to account for the lower SNR and increased CNR in the mprage. You'll need to look in the recon-all script for the details cheers Bruce On Thu, 30 May 2013, Caspar M. Schwiedrzik wrote: Hi! Is there more documentation on what settings the mprage flag enables in recon-all? Specifically, I would be interested which individual steps it affects and what the parameters are for each of the steps. Thanks! Caspar ___ 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] mprage flag in recon-all
I only find flags for mri_normalize and mri_segment in recon-all, and I have trouble reading the contents mri_normalize with a regular text editor. caspar 2013/5/31 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Caspar it changes some parameters to the intensity normalization and segmentation to account for the lower SNR and increased CNR in the mprage. You'll need to look in the recon-all script for the details cheers Bruce On Thu, 30 May 2013, Caspar M. Schwiedrzik wrote: Hi! Is there more documentation on what settings the mprage flag enables in recon-all? Specifically, I would be interested which individual steps it affects and what the parameters are for each of the steps. Thanks! Caspar 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/**compliancelinehttp://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] mprage flag in recon-all
yes, but recon-all just calls mri_segment with -mprage and mri_normalize with -mprage. I would like to know what -mprage does in these two functions, but i cannot search them because they are executables, not scripts. Caspar 2013/5/31 Harms, Michael mha...@wustl.edu Use any editor (even Word) with a search capacity, and search for the string 'mprage'. That will lead to you the variable internal to recon-all called IsMPRAGE. Searching for IsMPRAGE will then show you all in the stages that the -mprage flag affects. cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: Caspar M. Schwiedrzik cschwie...@mail.rockefeller.edu Date: Friday, May 31, 2013 2:14 PM To: Freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mprage flag in recon-all I only find flags for mri_normalize and mri_segment in recon-all, and I have trouble reading the contents mri_normalize with a regular text editor. caspar 2013/5/31 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Caspar it changes some parameters to the intensity normalization and segmentation to account for the lower SNR and increased CNR in the mprage. You'll need to look in the recon-all script for the details cheers Bruce On Thu, 30 May 2013, Caspar M. Schwiedrzik wrote: Hi! Is there more documentation on what settings the mprage flag enables in recon-all? Specifically, I would be interested which individual steps it affects and what the parameters are for each of the steps. Thanks! Caspar 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/**compliancelinehttp://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. -- The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return 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] mprage flag in recon-all
mri_normalize is a binary so you can't, just recon-all. On Fri, 31 May 2013, Caspar M. Schwiedrzik wrote: I only find flags for mri_normalize and mri_segment in recon-all, and I have trouble reading the contents mri_normalize with a regular text editor. caspar 2013/5/31 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Caspar it changes some parameters to the intensity normalization and segmentation to account for the lower SNR and increased CNR in the mprage. You'll need to look in the recon-all script for the details cheers Bruce On Thu, 30 May 2013, Caspar M. Schwiedrzik wrote: Hi! Is there more documentation on what settings the mprage flag enables in recon-all? Specifically, I would be interested which individual steps it affects and what the parameters are for each of the steps. Thanks! Caspar 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] mprage flag in recon-all
oh, my mistake. I thought it called them with specific parms. Sorry: for mri_segment: gray_hi = 99 ; (same as --ghi 99) wm_low = 89 ;(same as -wlo 89) for mri_normalize: intensity_below = 15 ; (same as -b 15) cheers Bruce On Fri, 31 May 2013, Caspar M. Schwiedrzik wrote: yes, but recon-all just calls mri_segment with -mprage and mri_normalize with -mprage. I would like to know what -mprage does in these two functions, but i cannot search them because they are executables, not scripts. Caspar 2013/5/31 Harms, Michael mha...@wustl.edu Use any editor (even Word) with a search capacity, and search for the string 'mprage'. That will lead to you the variable internal to recon-all called IsMPRAGE. Searching for IsMPRAGE will then show you all in the stages that the -mprage flag affects. cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: Caspar M. Schwiedrzik cschwie...@mail.rockefeller.edu Date: Friday, May 31, 2013 2:14 PM To: Freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mprage flag in recon-all I only find flags for mri_normalize and mri_segment in recon-all, and I have trouble reading the contents mri_normalize with a regular text editor. caspar 2013/5/31 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Caspar it changes some parameters to the intensity normalization and segmentation to account for the lower SNR and increased CNR in the mprage. You'll need to look in the recon-all script for the details cheers Bruce On Thu, 30 May 2013, Caspar M. Schwiedrzik wrote: Hi! Is there more documentation on what settings the mprage flag enables in recon-all? Specifically, I would be interested which individual steps it affects and what the parameters are for each of the steps. Thanks! Caspar 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. The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return 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.
