Re: [Freesurfer] question for preprocessing

[Bruce Fischl]

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:



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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.  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; 
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

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Re: [Freesurfer] question for preprocessing

[ping cao]

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.mgzbrainmask.mgz
> *orig.mgz * ctrl_pts.mgz
>*orig_nu.mgz  *

wm.asegedit.mgzaseg.auto_noCCseg.mgz   filled.mgz
>   rawavg.mgz wm.mgz

aseg.mgzlh.ribbon.mgz
>rh.ribbon.mgz wm.seg.mgz
>   aseg.presurf.hypos.mgz

ribbon.mgz   wmparc.mgz


Best,
ping

Greve, Douglas N.,Ph.D.  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;
> 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
>
> ___
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>
>
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Re: [Freesurfer] question for preprocessing

[Greve, Douglas N.,Ph.D.]

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



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Re: [Freesurfer] question about preprocessing and analysis in FS 4.5 vs FS5

[Douglas N Greve]

   If 4.5 will actually run on 5.0 preprocessed data, then I think it 
should be ok, but it has been a very long time since 4.5 so I can't say 
with any confidence.

doug

On 04/08/2015 01:33 PM, Katie Bettencourt wrote:
 I had a question about using different components of Freesurfer 4.5 
 and Freesurfer 5 in an analysis.  We were wondering whether it is 
 possible to do preprocessing in Freesufer 5, but run the analysis on 
 Freesufer 4.5 or whether the output from preprocessing in Freesurfer 5 
 is not compatible with the analysis methods in 4.5.  For reasons I 
 don't want to go into, it is not possible to switch to doing the 
 analysis in Freesurfer 5, but we would like to incorporate some of the 
 improvements in the preprocessing stream in Freesufer 5 if possible.  
 Any guidance would be appreciated.


 Katie Bettencourt

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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