# Correct registration in Slicer output to Freesurfer

**URL:** <https://discourse.slicer.org/t/correct-registration-in-slicer-output-to-freesurfer/31934>\
**Category:** Support\
**Tags:** registration, freesurfer\
**Created:** [September 27, 2023, 2:49pm UTC](https://discourse.slicer.org/t/correct-registration-in-slicer-output-to-freesurfer/31934 "2023-09-27T14:49:51Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Victor\_Zeng](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/victor_zeng/32/18303_2.png) [@Victor\_Zeng](https://discourse.slicer.org/u/Victor_Zeng)\
**Post date:** [September 27, 2023, 2:49pm UTC](https://discourse.slicer.org/t/correct-registration-in-slicer-output-to-freesurfer/31934/1 "2023-09-27T14:49:51Z")

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Hi all, for this project here, I am inputting into Slicer a brain image made in Freesurfer, namely the orig.mgz. Then I am managing manual segmentations done in Slicer using Segment Editor. Then I click on Export visible segments to binary labelmap and click on the resulting new labelmap export to file, and save as a .mgz file. When I use the freesurfer command:

tkmedit 1 orig.mgz -segmentation Slicerlabel.mgz, the Slicerlabel.mgz does not correct overlay with the orig.mgz.

(I know tkmedit is somewhat deprecated, but I think it wouldn’t overlay in freeview either)

Does anyone have any pointers on where to go?

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**Author:** ![pieper](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/pieper/32/8_2.png) [@pieper](https://discourse.slicer.org/u/pieper)\
**Post date:** [September 27, 2023, 5:29pm UTC](https://discourse.slicer.org/t/correct-registration-in-slicer-output-to-freesurfer/31934/2 "2023-09-27T17:29:06Z")

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If you haven’t already, you should try to use the SlicerFreeSurfer extension:

> **[GitHub - PerkLab/SlicerFreeSurfer: This repository contains the...](https://github.com/PerkLab/SlicerFreeSurfer)**
>
> This repository contains the SlicerFreeSurferImporter extension for 3D Slicer. The extension implements a module for importing models, scalar overlays, and segmentations from FreeSurfer, as well as...