Re: [Freesurfer] recon from 7T data
Hi Valeria Jon Polimeni and Andre van der Kouwe put together a specific acquisition and set of preprocessing steps for 7T (mp2rage I believe). You need to account for the transmit inhomogeneities, which are what is causing you to lose the temporal lobes. cheers Bruce On Mon, 25 Mar 2019, Barletta, Valeria wrote: Dear Freesurfers, I am trying to perform the FreeSurfer cortical reconstruction process from my 7 Tesla MEMPRAGE, but am getting very bad results (see first attachment) compared to what I had using the 3 Tesla images (second attachment). Before launching the "recon-all ... -all" command, I applied the FreeSurfer Gradient non-linearity correction. What can have been the problem? Thank you very much for your help, Valeria ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recon from 7T data
External Email - Use Caution Hi Valeria, you can account for the inhomogeneities Bruce was talking about by either using SPMs or FreeSurfers inhomogeneity correction. Personally, I prefer SPM over FreeSurfer, but if you supply a brainmask to the FreeSurfer tool, it gives reasonable results around the temporal lobes, too. I haven't used an MEMPRAGE sequence, however, using an MPRAGE you can use a FWHM of 30 and a regularization of 0.001 in SPMs segmentation tool, setting the sample distance to 2 improves the correction further. Using the N3 implemented in FreeSurfer you could run (from the subject's directory) mri_nu_correct.mni --n 2 --uchar transforms/talairach.xfm --mask brainmask.mgz --stop 0.0001 --distance 15 --fwhm 0.15 --shrink 2 --proto-iters 1 --i orig.mgz --o nu.mgz. Then proceed with the normalization of autorecon1. Both correction methods take quite some time. In case of MP2RAGE or if the MPRAGE was divided by a GRE manually you will need to adjust these settings accordingly. The N4 algorithm of ANTs works fine also if a brainmask is supplied. In case someone wants to have some parameters to run an inhomogeneity with that tool or on MP2RAGE/Division data, let me know. Best, Falk -Ursprüngliche Nachricht- Von: freesurfer-boun...@nmr.mgh.harvard.edu Im Auftrag von Bruce Fischl Gesendet: Montag, 25. März 2019 20:27 An: Freesurfer support list Cc: freesurfer-boun...@nmr.mgh.harvard.edu; Andre van der Kouwe ; Jonathan Polimeni Betreff: Re: [Freesurfer] recon from 7T data Hi Valeria Jon Polimeni and Andre van der Kouwe put together a specific acquisition and set of preprocessing steps for 7T (mp2rage I believe). You need to account for the transmit inhomogeneities, which are what is causing you to lose the temporal lobes. cheers Bruce On Mon, 25 Mar 2019, Barletta, Valeria wrote: > > > > > Dear Freesurfers, > > I am trying to perform the FreeSurfer cortical reconstruction process > from my 7 Tesla MEMPRAGE, but am getting very bad results (see first > attachment) compared to what I had using the 3 Tesla images (second > attachment). > > Before launching the "recon-all ... -all" command, I applied the > FreeSurfer Gradient non-linearity correction. > > > What can have been the problem? > > > Thank you very much for your help, > > Valeria > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recon from 7T data
thanks falk! and valeria, as for the SPM-based normalization, we also often use this for bias correction of 7 Tesla data, and natalia posted the parameters we use for 7T MPRAGEs here: https://surfer.nmr.mgh.harvard.edu/fswiki/HighFieldRecon -jon On Tue, 26 Mar 2019, falk.luesebr...@med.ovgu.de wrote: > External Email - Use Caution > > Hi Valeria, > > you can account for the inhomogeneities Bruce was talking about by either > using SPMs or FreeSurfers inhomogeneity correction. Personally, I prefer SPM > over FreeSurfer, but if you supply a brainmask to the FreeSurfer tool, it > gives reasonable results around the temporal lobes, too. > > I haven't used an MEMPRAGE sequence, however, using an MPRAGE you can use a > FWHM of 30 and a regularization of 0.001 in SPMs segmentation tool, setting > the sample distance to 2 improves the correction further. Using the N3 > implemented in FreeSurfer you could run (from the subject's directory) > mri_nu_correct.mni --n 2 --uchar transforms/talairach.xfm --mask > brainmask.mgz --stop 0.0001 --distance 15 --fwhm 0.15 --shrink 2 > --proto-iters 1 --i orig.mgz --o nu.mgz. Then proceed with the > normalization of autorecon1. Both correction methods take quite some time. > > In case of MP2RAGE or if the MPRAGE was divided by a GRE manually you will > need to adjust these settings accordingly. The N4 algorithm of ANTs works > fine also if a brainmask is supplied. In case someone wants to have some > parameters to run an inhomogeneity with that tool or on MP2RAGE/Division > data, let me know. > > Best, > Falk > > -Ursprüngliche Nachricht- > Von: freesurfer-boun...@nmr.mgh.harvard.edu > Im Auftrag von Bruce Fischl > Gesendet: Montag, 25. März 2019 20:27 > An: Freesurfer support list > Cc: freesurfer-boun...@nmr.mgh.harvard.edu; Andre van der Kouwe > ; Jonathan Polimeni > Betreff: Re: [Freesurfer] recon from 7T data > > Hi Valeria > > Jon Polimeni and Andre van der Kouwe put together a specific acquisition and > set of preprocessing steps for 7T (mp2rage I believe). You need to account > for the transmit inhomogeneities, which are what is causing you to lose the > temporal lobes. > > cheers > Bruce > > > On Mon, 25 Mar 2019, Barletta, Valeria wrote: > > > > > > > > > > > Dear Freesurfers, > > > > I am trying to perform the FreeSurfer cortical reconstruction process > > from my 7 Tesla MEMPRAGE, but am getting very bad results (see first > > attachment) compared to what I had using the 3 Tesla images (second > > attachment). > > > > Before launching the "recon-all ... -all" command, I applied the > > FreeSurfer Gradient non-linearity correction. > > > > > > What can have been the problem? > > > > > > Thank you very much for your help, > > > > Valeria > > > > > > > > > ___ > 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
