[Freesurfer] Freesurfer 7T MPRAGE
External Email - Use Caution Hi, I am trying to process 7T MPRAGE data (not MP2RAGE) using recon-all. In previous threads, a few people have suggested using SPM to correct for bias first and then running recon-all. Alternatively I saw a thread which suggests modifying the mri_nu_correct command https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg61913.html Can I edit the recon-all to run this alternative command and simply run recon-all? The threads are all really old and SPM is now SPM12 which integrates things. Is this modified bias correction inside FS as good as SPM ? I am mainly interested in thalamic segmentation. Are there others with the same issue? Thanks manoj Manoj Saranathan Associate Professor, Dept. of Medical Imaging University of Arizona Ph: 520-626-6531 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Freesurfer 7T MPRAGE
External Email - Use Caution Dear Manoj, in case you want to rely on tools provided with FreeSurfer only, N3 can produce good results even for 7T data. However, in my experience, you need to supply a brainmask to N3 to achieve very similar results compared to SPM. Otherwise, especially around the temporal lobes the inhomogeneity will not be corrected sufficiently. Tweaking recon-all for this is possible, but is slightly more complicated than changing the parameters of mri_nu_correct only. Furthermore, the procedure may change in case you use higher resolution 7T data. Apart from that SPM, N3 as well as N4 of ANTs (also using a brainmask) will all produce similar results. I mostly use SPM for pre-processing my 7T data as it is the easiest to use in my processing pipeline. Best, Falk Von: freesurfer-boun...@nmr.mgh.harvard.edu im Auftrag von Manoj Saranathan Gesendet: Montag, 6. Januar 2020 23:51:23 An: freesurfer@nmr.mgh.harvard.edu Betreff: [Freesurfer] Freesurfer 7T MPRAGE External Email - Use Caution Hi, I am trying to process 7T MPRAGE data (not MP2RAGE) using recon-all. In previous threads, a few people have suggested using SPM to correct for bias first and then running recon-all. Alternatively I saw a thread which suggests modifying the mri_nu_correct command https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg61913.html Can I edit the recon-all to run this alternative command and simply run recon-all? The threads are all really old and SPM is now SPM12 which integrates things. Is this modified bias correction inside FS as good as SPM ? I am mainly interested in thalamic segmentation. Are there others with the same issue? Thanks manoj Manoj Saranathan Associate Professor, Dept. of Medical Imaging University of Arizona Ph: 520-626-6531 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Freesurfer 7T MPRAGE
I also usually use spm intensity noramlization, but I think you could also use fsl. On 1/6/2020 11:45 PM, falk.luesebr...@med.ovgu.de wrote: > External Email - Use Caution > > Dear Manoj, > > > in case you want to rely on tools provided with FreeSurfer only, N3 can > produce good results even for 7T data. However, in my experience, you need to > supply a brainmask to N3 to achieve very similar results compared to SPM. > Otherwise, especially around the temporal lobes the inhomogeneity will not be > corrected sufficiently. > > > Tweaking recon-all for this is possible, but is slightly more complicated > than changing the parameters of mri_nu_correct only. Furthermore, the > procedure may change in case you use higher resolution 7T data. > > > Apart from that SPM, N3 as well as N4 of ANTs (also using a brainmask) will > all produce similar results. I mostly use SPM for pre-processing my 7T data > as it is the easiest to use in my processing pipeline. > > > Best, > > Falk > > > Von: freesurfer-boun...@nmr.mgh.harvard.edu > im Auftrag von Manoj Saranathan > > Gesendet: Montag, 6. Januar 2020 23:51:23 > An: freesurfer@nmr.mgh.harvard.edu > Betreff: [Freesurfer] Freesurfer 7T MPRAGE > > > External Email - Use Caution > > Hi, > > > I am trying to process 7T MPRAGE data (not MP2RAGE) using recon-all. In > previous threads, a few people have suggested using SPM to correct for bias > first and then running recon-all. Alternatively I saw a thread which suggests > modifying the mri_nu_correct command > > https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg61913.html > > > > Can I edit the recon-all to run this alternative command and simply run > recon-all? The threads are all really old and SPM is now SPM12 which > integrates things. Is this modified bias correction inside FS as good as SPM > ? I am mainly interested in thalamic segmentation. > > > Are there others with the same issue? > > > Thanks > > > manoj > > > Manoj Saranathan > Associate Professor, Dept. of Medical Imaging > University of Arizona > Ph: 520-626-6531 > > > > ___ > 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
