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the space in which the image was aqcuired.
Am Fr., 6. März 2020 um 18:31 Uhr schrieb Douglas N. Greve < dgreve@mgh.harvard.edu>:
what is "native space"?
On 3/6/2020 12:09 PM, Benjamin Ineichen wrote:
External Email - Use Cautionexample.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 CautionDear 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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-- ____________________________________ 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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