what is "native space"?
On 3/6/2020 12:09 PM, Benjamin Ineichen wrote:
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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
<dgr...@mgh.harvard.edu <mailto:dgr...@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:
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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
--
____________________________________
Benjamin Victor Ineichen, MD PhD
Karolinska Institutet
Center for Molecular Medicine
Stockholm, Sweden
ineic...@protonmail.ch <mailto:ineic...@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
ineic...@protonmail.ch <mailto:ineic...@protonmail.ch>
+41 76 391 04 01
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____________________________________
Benjamin Victor Ineichen, MD PhD
Karolinska Institutet
Center for Molecular Medicine
Stockholm, Sweden
ineic...@protonmail.ch <mailto:ineic...@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
ineic...@protonmail.ch <mailto:ineic...@protonmail.ch>
+41 76 391 04 01
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Freesurfer mailing list
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