What do you mean by "the average space of the subjects"?
On 3/24/2020 2:01 PM, Benjamin Ineichen wrote:
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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.ineic...@gmail.com <mailto:bv.ineic...@gmail.com>>:
the space in which the image was aqcuired.
Am Fr., 6. März 2020 um 18:31 Uhr schrieb Douglas N. Greve
<dgr...@mgh.harvard.edu <mailto:dgr...@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
<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
Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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
--
____________________________________
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
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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