The new Freesurfer has an optional flag to adjust NU intensity correction parameters for images acquired on 3T scanners. There exists also a flag for MPRage sequences.
I use 3T MPRages. What is the recommended use in this case?
Thanks Josh
Josh,
The new -3T flag affects the nu correction stage, and specifies a 3T-based target for the talairach alignment, and the existing -mprage flag affects mri_normalize and mri_segment, so you can use both.
Nick
The new Freesurfer has an optional flag to adjust NU intensity correction parameters for images acquired on 3T scanners. There exists also a flag for MPRage sequences.
I use 3T MPRages. What is the recommended use in this case?
Thanks Josh _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Regarding the -mprage tag, we read in the recon-all help that:
-mprage : assume scan parameters are MGH MP-RAGE protocol -washu_mprage : assume scan parameters are Wash.U. MP-RAGE protocol. both mprage flags affect mri_normalize and mri_segment, and assumes a darker gm
Would you recommend using -mprage for any MP-RAGE or just if you use the same protocol by Andre (that appears in the fs wiki and his website) ?
We are using a standard MP-RAGE sequence (not multiecho) with very similar parameters to the ones recommended by Andre, but not exactly the same.
Many thanks!, Gari
On Thu, Mar 7, 2013 at 1:54 AM, Nick Schmansky nicks@nmr.mgh.harvard.eduwrote:
Josh,
The new -3T flag affects the nu correction stage, and specifies a 3T-based target for the talairach alignment, and the existing -mprage flag affects mri_normalize and mri_segment, so you can use both.
Nick
The new Freesurfer has an optional flag to adjust NU intensity correction parameters for images acquired on 3T scanners. There exists also a flag for MPRage sequences.
I use 3T MPRages. What is the recommended use in this case?
Thanks Josh _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
-mprage is probably your best bet, but it would be worth trying out both ways and seeing the differences.
On Thu, 21 Mar 2013, Garikoitz Lerma-Usabiaga wrote:
Regarding the -mprage tag, we read in the recon-all help that:
-mprage : assume scan parameters are MGH MP-RAGE protocol -washu_mprage : assume scan parameters are Wash.U. MP-RAGE protocol. both mprage flags affect mri_normalize and mri_segment, and assumes a darker gm
Would you recommend using -mprage for any MP-RAGE or just if you use the same protocol by Andre (that appears in the fs wiki and his website) ?
We are using a standard MP-RAGE sequence (not multiecho) with very similar parameters to the ones recommended by Andre, but not exactly the same.
Many thanks!, Gari
On Thu, Mar 7, 2013 at 1:54 AM, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote: Josh,
The new -3T flag affects the nu correction stage, and specifies a 3T-based target for the talairach alignment, and the existing -mprage flag affects mri_normalize and mri_segment, so you can use both. Nick > The new Freesurfer has an optional flag to adjust NU intensity correction > parameters for images acquired on 3T scanners. There exists also a flag > for MPRage sequences. > > I use 3T MPRages. What is the recommended use in this case? > > Thanks > Josh
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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@nmr.mgh.harvard.edu
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Bruce Fischl -
Garikoitz Lerma-Usabiaga -
Joshua Lee -
Nick Schmansky