You can use ANTS N3 by adding -ants-n3 to the command line. In theory,
you can use a mask, but I vaguely remember that there was a bug when
someone tried it in our code
On 5/28/2020 12:37 PM, Schranzer René wrote:
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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:
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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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