Re: [Freesurfer] control point and aseg edit

Hello Bruce,

Yes, that is my end goal. I have a patient i edited the aseg to include left-cerebral white matter and also, want to normalize the intensity using expert option. Where should I place the "-canorm-usecps" flag ? After the command like " recon-all -autorecon2 -autorecon3 -expert -parallel -openmp 8 -bigventricles -3T time -canorm-usecps" or before autorecon2 like "recon-all -autorecon2 -canorm-usecps -autorecon3 -expert -parallel -openmp 8 -bigventricles -3T time. Thank you.

Best, Paul

On Thu, Sep 14, 2017 at 3:17 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

do you want the control points to be applied to the aseg? If so, you need to also specify -canorm-usecps

cheers Bruce On Thu, 14 Sep 2017, miracle ozzoude wrote:

Thanks Bruce. Yes, I want to regenerate the aseg and also use the expert

...

option for control point. That's recon-all -autorecon2 -autorecon3 -expert -parallel -openmp 8 -bigventricles -3T time. Best, Paul

On Thu, Sep 14, 2017 at 2:48 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: do you want it to regenerate the aseg? If not, then a). If so, then you would just run autorecon2 (instead of autorecon2-cp)

  cheers
  Bruce
  On Thu, 14 Sep 2017, miracle ozzoude wrote:

        I used the expert option for control points and manually

edited the aseg.presurf.mgz. Which is the proper flag to use in other to incorporate the respective changes? a) recon-all -autorecon2-cp -autorecon2-noaseg -autorecon3 -expert -parallel -openmp 8 -bigventricles -3T -time

        or

        b) recon-all -autorecon2-cp -autorecon3 -expert -parallel

-openmp 8 -bigventricles -3T -time

        Thanks.

        Best,
        Paul

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.