Dear Freesurfer experts,

I am aware that these are busy times. Please still allow me to repost my FreeSurfer problem:

I created manual masks on the Freesurfer input 001.mgz for several subjects. I would like to to transform all these individual masks to the average space of the subjects.

For this, I first ran mri_vol2vol:

mri_vol2vol --talres 1 --interp nearest --mov SW1-2039/BGmaskbin.nii.gz --s SW1-2039/001.nii --targ multiplems_average/mri/T1.mgz --regheader --o BG2039mask_avesp.mgz

The output from that was then used to run mri_robust register

mri_robust_register --mov BGmask2039_avesp.mgz --dst multiplems_average/mri/T1.mgz --lta BG_2039_reg.lta --mapmov BG_2039_reg.mgz --iscale --satit

But this does not seem to do the job.

How can I transform and register a mask to the average space?

Many thanks for your help!

Best regards,

Ben

Am Fr., 6. März 2020 um 18:33 Uhr schrieb Benjamin Ineichen <bv.ineichen@gmail.com>:

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:
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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 <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:
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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

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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Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--

____________________________________

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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--

____________________________________

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