# Misalignment between Freesurfer brain segmentation and original T1 images

**URL:** <https://discourse.slicer.org/t/misalignment-between-freesurfer-brain-segmentation-and-original-t1-images/35524>\
**Category:** Support\
**Tags:** segmentation, segmentations, segment-editor, freesurfer\
**Created:** [April 16, 2024, 12:03pm UTC](https://discourse.slicer.org/t/misalignment-between-freesurfer-brain-segmentation-and-original-t1-images/35524 "2024-04-16T12:03:00Z")\
**Posts on this page:** 3\
**Page:** 1

<div class="post-metadata">

**Author:** ![pablomac7](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/pablomac7/32/70064_2.png) [@pablomac7](https://discourse.slicer.org/u/pablomac7)\
**Post date:** [April 16, 2024, 12:03pm UTC](https://discourse.slicer.org/t/misalignment-between-freesurfer-brain-segmentation-and-original-t1-images/35524/1 "2024-04-16T12:03:00Z")

</div>

Slicer version: 5.6.1

Hello,

I am having problems when exporting a brain segmentation as a .seg.nrrd file, previously imported into 3D Slicer from Freesurfer. When I import the segmentation and the original MRI images into 3D slicer using FreeSurfer Importer, the alignment between both looks correct. However, when I try to export the segmentation as a .seg.nrrd file, the dimensions of the file (256,256,256) do not match those of the original MRI (192,240,256). I think this 256^3 cube is the default output format in Freesurfer, but I was wondering if it was possible to export the aligned segmentation directly from 3D slicer, as Slicer seems to align it perfectly. I read in another post that it is possible to do so by selecting the original images as the reference volume, but the exported .seg.nrrd file still contains a matrix with 256^3 shape. I would be super grateful for any pointers.

Best,

Pablo

---

<div class="post-metadata">

**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [April 16, 2024, 12:08pm UTC](https://discourse.slicer.org/t/misalignment-between-freesurfer-brain-segmentation-and-original-t1-images/35524/2 "2024-04-16T12:08:20Z")

</div>

3D Slicer uses the same geometry (origin, spacing, axis directions, extents) for segmentation as the source volume. Therefore, if your input volume was 256 x 256 x 256 size then the segmentation will use that size by default. If for some reason the geometry does not match (e.g., becasue you selected a different image first, you chose the option to crop to minimum necessary size on save, you created a segmentation in an older Slicer version where we cropped to minimum necessary size by default, etc.) then you can very easily change it using [Specify geometry](https://slicer.readthedocs.io/en/latest/user_guide/modules/segmenteditor.html#main-options) feature.

---

<div class="post-metadata">

**Author:** ![pablomac7](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/pablomac7/32/70064_2.png) [@pablomac7](https://discourse.slicer.org/u/pablomac7)\
**Post date:** [April 16, 2024, 12:20pm UTC](https://discourse.slicer.org/t/misalignment-between-freesurfer-brain-segmentation-and-original-t1-images/35524/3 "2024-04-16T12:20:44Z")

</div>

Dear Andras,

Thank you so much for your answer, this is exactly what I needed. I hope this information will be useful to others as well.

Best,

Pablo