External Email - Use Caution Hi Bruce,
Many thanks for your reply. I understand from your answer that it could be done as follows (I am not an expert in FreeSurfer directives): a) run full FreeSurfer pipeline recon-all -s FOO b) insert pre-existing WM segmentation as wm.mgz (modifying the intensity values) c) re-run stages 15-23 and 24-31 (recon-all shall use my external segmentation as WM "edits") recon-all -s FOO -autorecon2-wm -autorecon3 Is it possible however to just include the WM segmentation without executing a full early run of recon-all? Thanks, Jordi On Tue, Nov 26, 2019 at 3:08 PM Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Jordi > > yes, this should be possible. You might need to run recon-all in stages > though. Although if you set the wm.mgz values from SPM to 255 and 1 (not > 0) > recon-all should detect them as "edits" and retain them > > cheers > Bruce > > > On Tue, 26 Nov 2019, Jordi Huguet wrote: > > > > > External Email - Use Caution > > > > Hi there, > > I wonder if its somehow possible to feed FreeSurfer's recon-all with > pre-existing segmented maps > > (based on prior segmentation procedure e.g. SPM or ANTs) to > "improve" FreeSurfer results. > > > > For some images I am working with the FreeSurfer's WM segmentation > output is not optimal so I am > > looking for alternatives to improve the final results on such specific > cases without requiring any > > manual intervention. > > > > Any comments, examples or shared reflections on this regard are kindly > welcome. > > > > Thanks in advance, > > Jordi Huguet > > > >_______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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