Can Mindboggle use output from prior versions of FreeSurfer?

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On Fri, Feb 24, 2017 at 6:55 AM Ritobrato Datta wrote:
Hi Arno,

This is fascinating stuff. In my research, I have come across instances when I felt that a hybrid of ANTS and freesurfer would be very useful. Is this pipeline possible for data processed with the earlier versions of freesurfer say 5.1 ? FS6 just got released in Jan 2017 and I am sure for most ongoing studies, the data have already been processed in earlier versions of freesurfer.

If there is a patch or script to update the data processed using earlier versions of freesurfer, that will save a lot of time than running everything from scratch in FS6.

Please let us know.



Great question! You can certainly run Mindboggle on FreeSurfer output for earlier versions of FreeSurfer. In fact, we did this for part of the work described in the PLoS Computational Biology article:

“For this study we used FreeSurfer v5.1-derived labels and meshes, but the recently released FreeSurfer version 6 is recommended because it uses Mindboggle’s DKT-100 surface-based atlas (with the DKT31 labeling protocol) by default to generate labels on the cortical surfaces, and generates corresponding labeled cortical and non-cortical volumes (wmparc.mgz) [75].”

I am certain you can run a FreeSurfer command to update the cortical labels to be in accord with the DKT-31 labeling protocol ( and the new DKT-100 atlas used in FreeSurfer. I will leave it to others on this list who have greater FreeSurfer expertise than I to recommend the appropriate command.