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Hi Douglas,
Thanks for your help!
Two more questions:
Is it possible to use the individual brain mask of my skull stripped data as a
"mask image" for the step of the NU Intensity correction in recon-all with an
additional flag to carry out a better bias correction?
And is it possible to use ANTsN3 instead of ANTsN4, if someone wants it?
Best,
René
Von: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> Im Auftrag von Douglas N. Greve
Gesendet: Donnerstag, 28. Mai 2020 17:47
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] Recon-all error in CA Normalize (FreeSurfer V 7.1)
You can use it with all subjects then
On 5/28/2020 3:28 AM, Schranzer René wrote:
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All subjects.
Best,
René
Von:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
Im Auftrag von Douglas N. Greve
Gesendet: Mittwoch, 27. Mai 2020 18:37
An: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Betreff: Re: [Freesurfer] Recon-all error in CA Normalize (FreeSurfer V 7.1)
Are all your subjects skull stripped or just this one?
On 5/24/2020 9:08 AM, Schranzer René wrote:
External Email - Use Caution
Hi Douglas,
First of all, thank you for your help.
I forgot to mention that I am already using skull-stripped data for the
recon-all processing stream. Therefore, I stopped after -autorecon1 and copied
the T1.mgz to brainmask.mgz and brainmask.auto.mgz and continued processing
with -autorecon2 and -autorecon3. In some subjects (at some timepoints), the
recon-all -autorecon2 -autorecon3 excited with errors, as mentioned below. Now
I have used the following command "recon-all -hires -skullstrip -no-wsgcaatlas
-s ${sbjID} -i ${sbj} -all" with the skull-stripped data and it worked fine
without errors. I also compared the T1.mgz from both approaches and they looked
identical.
My question, can I use this approach with the "-no-wsgcaatlas" for all subjects
or is there something to consider here?
Best, René
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