What is example.mgz?

If you want to transfer the orig.mgz, you can do it with
mri_vol2vol --tal --talres 1 --interp nearest --mov orig.mgz --s subject --o example.mni305.mgz



On 2/20/2020 3:53 PM, Benjamin Ineichen wrote:

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Dear Freesurfer experts,

In order to transform a segmentation mask (example.mgz) from native so standard MNI space I ran:
mri_vol2vol --talres 1  --interp nearest --mov example.mgz --s 001.mgz --targ $FREESURFER_HOME/subjects/fsaverage/mri/orig.mgz --regheader --o example.mni305.mgz

the output example.mni305.mgz did somehow transform to a different space as you can see in Screenshot orig where the native mask is white and the transformed mask is red. However, the masks seems to be in a completely different brain region in the native MNI space (Screenshot MNI). But the point of transforming my segmentation mask is that the segmented mask should be in the same brain region but just transformed to the standard space. How can I correct this?

Many thanks for the support!

/Ben

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____________________________________
Benjamin Victor Ineichen, MD PhD
Karolinska Institutet
Center for Molecular Medicine
Stockholm, Sweden
+41 76 391 04 01

Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen
Karolinska Institutet
Center for Molecular Medicine
Stockholm, Sweden
+41 76 391 04 01

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