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

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