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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu *Im Auftrag von *Douglas N. Greve *Gesendet:* Mittwoch, 27. Mai 2020 18:37 *An:* 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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