Dear Bruce,

I'm following your advice and now have replaced wm.mgz. Could you please let me know what options I should add to recon-all so not to overwrite my wm.mgz and get things going from this point? ( I have already run the recon-all so just need to re-run it with the replaced wm.mgz)

aseg.mgz is not a problem at all.

Thank you

James

On Thu, Dec 3, 2015 at 1:43 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

Hi James

what kind of segmentation? If gray/white you could replace the wm.mgz and go from there, otherwise you would replace the aseg.mgz. In either case, make sure you use our conventions (the FreeSurferColorLUT.txt for the aseg, or set every wm voxel to the brain.mgz intensity if it is in the white matter, and zero otherwise)

cheers
Bruce

On Thu, 3 Dec 2015, james pardon wrote:

Dear All,
I was wondering whether there is a simple way to pass T1 segmentations I have from another software
to Freesurfer, in order to do the remaining recon-all steps?

Thank you in advance,
James

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