1,recon-all ?Cautorecon1  (Stages 1-5)

2,Check talairach transform, skull strip, normalization (?)

3,recon-all ?Cautorecon2  (Stages 6-23)

4,Check surfaces

(1)Add control points: recon-all ?Cautorecon2 (Stages 10-23)

(2)Edit wm.mgz: recon-all ?Cautorecon2-wm (Stages 13-23)

(3)Edit brainmask.mgz: recon-all ?Cautorecon-pial (Stage 23)

5,recon-all ?Cautorecon3 (Stages 24-30)

Note: all stages can be run individually (this note was also from the slice)

 

But on the trouble shooting wiki page http://freesurfer.net/fswiki/FsTutorial/TroubleshootingData , the order is

1, edit brain mask

2, edit wm volume

3, correcting topological defects

4, skull strip

5, control point

6, talairach transformation

7, edit aseg

 

My quesion is, shouldn't I stick to the stages 1-30 order? I mean, I think results from earlier stages will influence later stages, so once an earlier stage output was edited, all the following steps should re-run, right? why talairach transformation can be checked later, which I think one should redo nearly every thing, right?

Or, are the 7 trouble shooting steps independ from each other, and I can edit in any order i want then re-run all necessary steps?

For example, should I edit wm and brian mask together, then run recon-all ?Cautorecon2, or should I edit wm and run recon-all ?Cautorecon2 then edit brainmask and run recon-all ?Cautorecon-pial?

 

Thanks for any help!

 

Best~

 

 

Dear FreeSurfer List,

I like to introduce you to a new set of reference brain networks

(cognitive components) estimated from 10,449 experiments and 83

behavioral tasks from the BrainMap database, which can be downloaded

here: https://surfer.nmr.mgh.harvard.edu/fswiki/BrainmapOntology_Yeo2015.

The networks will be incorporated in some future version of

FreeSurfer.

Since these networks are estimated from (meta-analytic) task data,

they are meant to complement (not replace) the current resting-state

networks in FreeSurfer

(https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011)

Cheers,

Thomas

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