Dear Manuel, I would chime in with my current experience with transfering v5.3 reconstructions to v6.0: The wm segmentation results (and therefore white/pial surfaces, apart from other things) are different between versions, especially in ambiguous areas and especially if there is a difference in interpolation during conform step (in v 6.0 the cubic interpolation is off; if it is off or on in v5.3 it depends on whether you used patched version of recon-all or not). It of course also depends on the quality of your data.
In any case, my experience is, if you want to keep high quality of your results, you probably would need to re-inspect your data again and correct newly appeared errors in surfaces. Antonin Skoch all the edits will be taken into account regardless of what command line args you use On 6/9/17 3:08 AM, Manuel Delgado wrote: Dear all, Regarding this issue: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51931.html we have the same situation. We are going to reprocess data previously processed with FS 5.3. If we proceed with *recon-all -all *will all the edits be taken into account (i.e. skull strip, control points, wm and pial edits) or is it necessary to proceed with ordered steps (i.e -autorecon-pial, then -autorecon2-cp autorecon3, and so on)? Thanks in advance, Manuel
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