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

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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

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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.

Thanks Bruce. resetting means, all my changes will be incorporated into the final output files?

Best, Paul

On Thu, Sep 14, 2017 at 3:52 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

I'm not sure it matters, but if you put it at the end nothing will reset it

On Thu, 14 Sep 2017, miracle ozzoude wrote:

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



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        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.

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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.

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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.

Thank you very much Bruce.

Best, Paul

On Thu, Sep 14, 2017 at 4:02 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

I mean there will be no subsequent command that turn of the use of control points in the aseg

cheers Bruce

On Thu, 14 Sep 2017, miracle ozzoude wrote:

Thanks Bruce. resetting means, all my changes will be incorporated into

...

the final output files? Best, Paul

On Thu, Sep 14, 2017 at 3:52 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: I'm not sure it matters, but if you put it at the end nothing will reset it On Thu, 14 Sep 2017, miracle ozzoude wrote:

        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



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                    https://mail.nmr.mgh.harvard.e

du/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.

        _______________________________________________
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        The information in this e-mail is intended only for the

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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.