External Email - Use Caution
Dear expert，
Thank you for reading!
I want to do these four pre-processing steps:
1. Re-sampling each MR image to 256*256*256; 2. Using the N3 algorithm for intensity inhomogeneity correction;
3. Skull stripping;
4. Removing the cerebellum.
Does " *recon-all"* do all the above 4 steps automatically? If so, which file is just finished with these four steps? If not, how can I do these steps?
Your help is greatly appreciated.
Best, ping
It does 1-3. It also labels cerebellum which you could then use to perform #4
On 6/23/2019 7:03 AM, ping cao wrote:
External Email - Use Caution
Dear expert，
Thank you for reading!
I want to do these four pre-processing steps: 1. Re-sampling each MR image to 256*256*256; 2. Using the N3 algorithm for intensity inhomogeneity correction; 3. Skull stripping; 4. Removing the cerebellum. Does " recon-all" do all the above 4 steps automatically? If so, which file is just finished with these four steps? If not, how can I do these steps?
Your help is greatly appreciated.
Best, ping
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Thank you for your reply. I also want to know which file has just finished with 1-3 steps? Is it nu.mgz? Or nu.mgz?
*T1.mgz * aseg.presurf.mgz
aparc+aseg.mgz brain.finalsurfs.mgz * norm.mgz
aparc.DKTatlas+aseg.mgz *brain.mgz *
*nu.mgz* aparc.a2009s+aseg.mgz brainmask.auto.mgz
aseg.auto.mgz brainmask.mgz
*orig.mgz * ctrl_pts.mgz *orig_nu.mgz *
wm.asegedit.mgz aseg.auto_noCCseg.mgz filled.mgz
rawavg.mgz wm.mgz
aseg.mgz lh.ribbon.mgz
rh.ribbon.mgz wm.seg.mgz aseg.presurf.hypos.mgz
ribbon.mgz wmparc.mgz
Best, ping
Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu 于2019年6月23日周日 下午9:35写道：
It does 1-3. It also labels cerebellum which you could then use to perform #4
On 6/23/2019 7:03 AM, ping cao wrote:
External Email - Use CautionDear expert，
Thank you for reading!
I want to do these four pre-processing steps:
Re-sampling each MR image to 256*256*256;
Using the N3 algorithm for intensity inhomogeneity correction;
Skull stripping;
Removing the cerebellum.
Does " *recon-all"* do all the above 4 steps automatically? If so, which file is just finished with these four steps? If not, how can I do these steps?
Your help is greatly appreciated.
Best, ping
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
well, we don't run only those steps to generate any volume. Probably your best bet would be the norm.mgz, although as Doug says it will have a cerebellum in it, which you can strip with the aseg.mgz
cheers Bruce
On Sun, 23 Jun 2019, ping cao wrote:
External Email - Use Caution
Thank you for your reply.I also want to know which file has just finished with 1-3 steps? Is it nu.mgz? Or nu.mgz? T1.mgz aseg.presurf.mgz aparc+aseg.mgz brain.finalsurfs.mgz norm.mgz
aparc.DKTatlas+aseg.mgz brain.mgz nu.mgz aparc.a2009s+aseg.mgz brainmask.auto.mgz aseg.auto.mgz brainmask.mgz orig.mgz ctrl_pts.mgz orig_nu.mgz wm.asegedit.mgz aseg.auto_noCCseg.mgz filled.mgz rawavg.mgz wm.mgz aseg.mgz lh.ribbon.mgz rh.ribbon.mgz wm.seg.mgz aseg.presurf.hypos.mgz ribbon.mgz wmparc.mgzBest, ping
Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu 于2019年6月23日周日 下午9:35写道： It does 1-3. It also labels cerebellum which you could then use to perform #4
On 6/23/2019 7:03 AM, ping cao wrote: External Email - Use Caution Dear expert， Thank you for reading! I want to do these four pre-processing steps: 1. Re-sampling each MR image to 256*256*256;
Using the N3 algorithm for intensity inhomogeneity correction;
3. Skull stripping; 4. Removing the cerebellum.Does " recon-all" do all the above 4 steps automatically? If so, which file is just finished with these four steps? If not, how can I do these steps?
Your help is greatly appreciated.
Best, ping
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Greve, Douglas N.,Ph.D. -
ping cao