example.mgz is just some example mask created on a template in native space. And I would need to transform it to MNI space. Thus, 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 transformed mask (example.mni305) is located in a completely different brain region in the MNI template compared to the native mask in the native template (see screenshots). How I can I correct this? Do I need to register the native and MNI template first?

Thanks!

/Ben

Am Fr., 6. März 2020 um 17:59 Uhr schrieb Douglas N. Greve <dgreve@mgh.harvard.edu>:

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:
External Email - Use Caution

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

--

____________________________________

Benjamin Victor Ineichen, MD PhD

Karolinska Institutet

Center for Molecular Medicine

Stockholm, Sweden

ineichen@protonmail.ch

+41 76 391 04 01

Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen

Karolinska Institutet

Center for Molecular Medicine

Stockholm, Sweden

ineichen@protonmail.ch

+41 76 391 04 01
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