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


On Tue, 26 Nov 2019, Jordi Huguet wrote:

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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

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