External Email - Use Caution Dear Malte Thank you so much. I've tried both rigid and affine transformations, and I've attached a snapshot that shows how the CC doesn't fully overlap with the template. I'm using a high-quality DTI image and am wondering if incorporating a T1 image would help improve the registration. I'm not sure how to apply a two-step registration, if that's even possible, using mri_synthmorph. Thanks for your guidance.
Best, John On Fri, Sep 1, 2023 at 1:27 PM Hoffmann, Malte,PhD < mhoffm...@mgh.harvard.edu> wrote: > External Email - Use Caution > > Hi John, > > Currently, the default transformation model is "deform". Could you check > if "affine" yields a better result? > > mri_synthmorph -m affine fa.nii.gz template.nii.gz -o fa_in_MNI.nii.gz > > Cheers, > Malte > > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of John Anderson < > jb19790...@gmail.com> > Sent: Friday, September 1, 2023 12:45 > To: Freesurfer support list > Subject: [Freesurfer] mri_synthmorph > > External Email - Use Caution > > Dear Freesurfer experts, > I processed DTI data using dt_recon, and I want to register FA images to > the standard MNI152 space. However, after running the command > mri_synthmorph fa.nii.gz template.nii.gz -o fa_in_MNI.nii.gz, > > the registration is not accurate. I'm not sure what I've done wrong. Thank > you for any guidance. > > sincerely > J > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1bk1jbPW069aqrMXRWR0gk1CdmugoB607jxsaBNmUbtiFJunF7psUi_c3uIm3bkV-V_JXO6XqXWHmiRM6VTfwDkJCrWK0Mecrmmy3YICYFwu43V0nJu1li_OxnnOuvNgTw0V09WWNuFii_NMj1WC8_Hf72V-4UwABgCD8GnPO3hNC4KH5eiJilko2W_znu15Gsu-A3nlWRD_e8QuTEkqu2FWedOcGeTyrjHcfaOsJQOb_tVC2wX0FrTL0OtfvUZgNBNW4msoj0n8WvvtnB9kg5KkFqNRQ7ThmMJCqyvBz6lCV3Bet4TKnck2Ph9UbQSbWWWX1KrpjsGyaQQ9RrcjlAQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > 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 Mass General > Brigham Compliance HelpLine at > https://secure-web.cisco.com/1OhLWc08Q0-Z6vg0PUzLX0EzcQ1aYGzygiuxmzGiyBmXugoLvVDxNIQVmG3yRg2vuFBIYxJfBtpdNyRPBagy-SY8JibbuSTJRSOm60WYT_ZsTW_JbPpHbQrHVLpYuKC4oA4kbVsItWqHb1l2AvuQY_SlsQXRMPChkvYwjVUgo8Ym3nmhMI_PveVKy5jOUrg7OtQS-IwdiOrvN8Av9zQlfXDopDCJCMWPEvQ2LwWkhr833wO5mbJuywZtaPTQxuLx6K9P-0t2atHwUkh_44uMcKbgxOuI8oa4uPBoRvNyOjZIUHXm848FupEiJguWTPS2IY-4SD8jfui05l4_ZHXEFoQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > < > https://secure-web.cisco.com/1OhLWc08Q0-Z6vg0PUzLX0EzcQ1aYGzygiuxmzGiyBmXugoLvVDxNIQVmG3yRg2vuFBIYxJfBtpdNyRPBagy-SY8JibbuSTJRSOm60WYT_ZsTW_JbPpHbQrHVLpYuKC4oA4kbVsItWqHb1l2AvuQY_SlsQXRMPChkvYwjVUgo8Ym3nmhMI_PveVKy5jOUrg7OtQS-IwdiOrvN8Av9zQlfXDopDCJCMWPEvQ2LwWkhr833wO5mbJuywZtaPTQxuLx6K9P-0t2atHwUkh_44uMcKbgxOuI8oa4uPBoRvNyOjZIUHXm848FupEiJguWTPS2IY-4SD8jfui05l4_ZHXEFoQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> > . > >
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
