Hi Nazanin

1. The registration is only one step in how we do segmentation, so I wouldn't suggest just using it. If you can convert your registration to .m3z format and put it in the subjects transforms/talairach.m3z you could try running from there forward.

2. Yes, you can edit the aseg in freeview.

3. Yes, the segmentations have improved in V6

cheers Bruce On Wed, 8 Nov 2017, N Saf wrote:

Hi Bruce as you explain I did the registration somewhere else and now I have the labels_gca in my subject space.

1. is it possible to somehow import this file in freesurfer and run the rest of the analysis ?

2.my question in general is that : can I in anyway  do any correction for aseg outputs during the analysis(similar to troubleshooting for surface-base analysis) e.g. do some step with different method and then import the result and use the rest steps in freesurfer?? 3.Is there any difference between the subcortical segmentation results in v.6  vs v5.3 (except the hippopotamus subfields segmentation which is available in v.6 . Is the hole hippocampus volume result  different between 2 versions?)

I'm really appreciated for the help.

Best Regards, Nazanin

On Mon, Oct 30, 2017 at 5:36 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Nazanin

  the nonlinear registration is actually to our segmentation atlas (*.gca). I guess you
  could try using something else, but you should extract a mean intensity image from the
  gca as a target, not the MNI305. You can do this with:

  mri_convert -nth 0 <file>.gca mean_gca.mgz

  FYI, this:

  mri_convert -nth 1 <file>.gca labels_gca.mgz

  would give you the highest prior label at each spot (and 2 would give you the prior)

  cheers
  Bruce



  On Mon, 30 Oct 2017, N Saf wrote:

        Dear Experts,
        In the volume-based stream, if I'm right the FreeSurfer does two
        registration with MNI305 ,one affine and one
        nonlinear , is it possible to perform the nonlinear registration somewhere
        else and then use the result in
        FreeSurfer and run the rest of the analysis ? 

        thank's alot for your great support.

        BRG,
        Nazanin

---

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.