Still wondering about this - thanks in advance for any help!

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Makaretz, Sara Johanna [SMAKARETZ@mgh.harvard.edu] Sent: Thursday, June 01, 2017 21:30 To: Freesurfer support list Subject: Re: [Freesurfer] Difference between -autorecon2-wm and -autorecon2-noaseg ?

Adding to this question, I'm wondering whether it's appropriate to do both wm & aseg.presurf edits at the same time, and (if yes) whether there is a difference between reprocessing the recon with -autorecon2-noaseg or -autorecon2-wm

ie. Hypothetically, a subject with big ventricles is processed in FS v6.0 stable with the flag -bigventricles. The initial recon has wm surfs that dip into the posterior horn of the lateral ventricle.

1st edits: fill ventricle on wm.mgz (and other wm edits in other regions); reprocess w -autorecon2-wm -autorecon3 wm surfs around posterior horn of ventricle not corrected

2nd edits: in aseg.presurf.mgz, relabel problem voxels from cortex -> wm; if just these edits, reprocess w -autorecon2-noaseg -autorecon3

But if the subject has wm.mgz errors in other regions, can those edits be be made together? And would it matter whether the recon is reprocessed with -autorecon2-wm or -autorecon2-noaseg?

Thanks for any advice!

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Makaretz, Sara Johanna [SMAKARETZ@mgh.harvard.edu] Sent: Tuesday, May 23, 2017 14:31 To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Difference between -autorecon2-wm and -autorecon2-noaseg ?

Hi,

I'm using FS v6.0 stable. Is there any difference between running recon-all with -autorecon2-wm or -autorecon-noaseg? It looks like both are starting at -normalization2 and running through the rest of autorecon2 with no changes to inputs/args compared to "regular" -autorecon2.

Is this true, and can I use -autorecon2-wm and -autorecon2-noaseg interchangeably?

https://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFlags https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0

Thanks! Sara