Re: [Freesurfer] Creating own atlas

Hi Bruce, I'm using v5.3.0. Does this version do well with patients with large ventricles? Two cases I ran seemed to do well with the ventricles, but some others seem to be running into some errors (which I haven't had the time to work out yet). So in your opinion, to get our desired measures of total gray matter and ventricular volume, we would not need to create our own atlas?

Side question: Is there any literature on/do you happen to know what the margin of error for a measure like total gray matter (taken from the aseg.stats header) is in Freesurfer?

Thanks, Brianna

On Fri, Jul 11, 2014 at 10:34 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

Hi Brianna

yes, that would work (although you would use freeview or tkmedit).

Why do you feel you need a new atlas? Our latest version does quite well, even on subjects with very very large ventricles. What version are you running?

cheers Bruce

On Fri, 11 Jul 2014, Brianna Damadian wrote:

Hi Bruce, Would be interested in an atlas for aseg that gives total gray

...

matter and ventricle volume. Would I be able to create an atlas based on these 30 patients with labeled volumes for just these measures? Additionally, my understanding of creating an atlas is very rudimentary - would I begin the process by running recon-all on these 30 scans and then manually editing the segmentations using tksurfer?

Thanks again, Brianna

On Fri, Jul 11, 2014 at 10:14 AM, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote: Hi Brianna

  what kind of atlas do you mean? If one for creating the aseg you

will need to have labeled volumes for creating a new atlas

  cheers
  Bruce


  On Fri, 11 Jul 2014, Brianna Damadian wrote:

  > Hello,
  >
  > I am interested in creating my own atlas for elderly patients

with enlarged ventricles. We have about 30 patients with axial MPR scans. Is this enough to build an atlas? > > Thanks, > Brianna > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ 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.