Dear Erik, I never put together a multi-spectral version of the brainstem segmentation because, given the coarse structures that we segment (midbrain, pons, medulla, scp), there’s pretty much nothing to be gained from additional contrasts.
In terms of registration: if your “small volume” is acquired during the same session as the 1mm T1 you’ve processed with FreeSurfer, they should be almost overlapping in RAS coordinates. You can then use mri_robust_register with the —noinit flag to register the volumes. I would strongly encourage you to use the small volume as target of the registration and the 1mm T1 as source; you can always invert the resulting rigid transform matrix to go in the other direction. Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com On Sep 20, 2021, at 18:43, Erik O'Hanlon <ohanl...@tcd.ie<mailto:ohanl...@tcd.ie>> wrote: External Email - Use Caution External Email - Use Caution Dear Experts, We hope to acquire some multishell dwi and structural data to investigate tracts passing through the Locus Coeruleus (LC) and we want to apply the brainstem segmentation to our structural data to obtain subject specific LC masks. Is it possible to feed multispectral data into the brainstem segmentation ? Is it possible to acquire a high res volume capturing the LC in greater detail and co-register that to the whole brain T1 (T2 or FLAIR ) to further assist in the delineation of the LC roi and quantification of the LC volume? If it's possible to use an additional small volume like this, do I need to pre-process it using recon-all and what is the optimal way to co-register the small volume to the whole brain T1 to assist in the mask generation? Any guidance is very much appreciated. Best regards and thanks, Erik _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://secure-web.cisco.com/1e0K0Qpt0HADjYKHLwxppb4VSEbFeiC_dzSdIRHl2SDVei2h5UnWj-3vTHhN3pQNH5dTWqo-lu63OpinjMFQT0UUQlI8CHL3PRPCbDoyAEpNMabaTXXe6RgREyKlF8obA7SpvgXD1KpOMw5_jP2A_ZIoPdNyW5Np--AZuEet24QMc0-7gcoxz-3G3wwdy2tmLYMK2gd65icEt_cJkFdIdS8Uow2kUYcrAi7WrOEt3Cn2Vg07g3nO09LK0Jv2Y8MX9VTG0wXPDt9CfmqSfnUrdXw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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