Misalignment between Freesurfer brain segmentation and original T1 images

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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

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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 feature.

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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

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