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 http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005350#pcbi.1005350.ref075 ]."

I am certain you can run a FreeSurfer command to update the cortical labels to be in accord with the DKT-31 labeling protocol ( http://journal.frontiersin.org/article/10.3389/fnins.2012.00171/full) 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.

Cheers, Arno

On Fri, Feb 24, 2017 at 6:55 AM Ritobrato Datta ridatta@mail.med.upenn.edu 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.

Best

Rito

----- Original Message ----- From: Arno Klein binarybottle@gmail.com To: freesurfer@nmr.mgh.harvard.edu Sent: Thu, 23 Feb 2017 20:37:44 -0500 (EST) Subject: [Freesurfer] Mindboggle official software release and publication!

Announcing the official release of Mindboggle (http://mindboggle.info), open source software http://mindboggle.info/software.html and data https://osf.io/ydyxu/ for analyzing the shapes of brain structures from human MRI data (processed through FreeSurfer and optionally through ANTs). The release coincides with a publication in PLoS Computational Biology that documents and evaluates the software:

Klein A, Ghosh SS, Bao FS, Giard J, Hame Y, Stavsky E, Lee N, Rossa B, Reuter M, Neto EC, Keshavan A. (2017) Mindboggling morphometry of human brains. PLoS Computational Biology 13(3): e1005350. doi:10.1371/journal.pcbi.1005350 http://doi.org/10.1371/journal.pcbi.1005350

Cheers, @rno

Thanks to Docker, you can run it on a mac, it's all explained on the Mindboggle website.

Olivier

Shane Schofield a écrit :

Hello,

Thanks. Seems very interesting! Is there any way to run this on Mac?

Cheers

-- Shane Schofield _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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