HI Pascal

I got significantly improved results using -b 20 on the mri_normalize command line. Note that this has to come after the mprage. I think you can do it with an expert options file with:

mri_normalize -b 20

cheers
Bruce

On Fri, 3 Feb 2017, Pascal Goodman wrote:

Hello Bruce, I sent it. 
Pascal

On Fri, Feb 3, 2017 at 11:26 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
      https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange

      tar and gzip an example subject directory and send us the voxel coords of points you want us
      to look at

      cheers
      Bruce
      On Fri, 3 Feb 2017, Pascal Goodman wrote:

            Thanks bruce. Do I upload the entire file? Also,where can I find the
            link? Pascal

            On Fri, Feb 3, 2017 at 10:35 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu>
            wrote:
                  Hi Pascal

                  I don't think tissue priors will help due to the complexity and
            variability of the folding
                  patterns. There may be other interventions though - can you send us some
            examples of where
                  things don't look accurate to you?

                  cheers
                  Bruce


                  On Fri, 3 Feb 2017, Pascal Goodman wrote:

                        Hello Bruce, Thanks for replying. I am trying find ways to improve
            white matter
                        surface (to reduce
                        manual intervention by control points) with the probability map.
            Also, how do I
                        extract the multiple
                        prior maps you mentioned. Thank you. 
                        Best, 
                        Pascal

                        On Fri, Feb 3, 2017 at 10:22 AM, Bruce Fischl
            <fischl@nmr.mgh.harvard.edu>
                        wrote:
                              Hi Pascal

                              what are you trying to achieve? Internally we have multiple
            prior maps of
                        this type, but I
                              don't think we are setup for a user to supply a different one

                              cheers
                              Bruce

                              On Fri, 3 Feb 2017, Pascal Goodman wrote:

                                    Hello Freesurfer, I do have a question. Can FS take
            probability maps
                        of  tissue
                                    segmentation as prior? 
                                    Thanks, 
                                    Pascal



                        _______________________________________________
                        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.




_______________________________________________
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.