oK, this will not be that pretty, but you can
mri_vol2vol --mov yourRoi.mgz --targ orig.mgz --interp nearest
--regheader --o yourRoiOrig.mgz
mri_convert yourRoiOrig.mgz yourRoiOrigAverageSpace.mgz
--apply_transform subject/mri/transforms/talairach.xfm -rt nearest
On 3/27/2020 11:03 AM, Benjamin Ineichen wrote:
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The space i created from all subjects using make_average_subject.
Douglas N. Greve <dgr...@mgh.harvard.edu
<mailto:dgr...@mgh.harvard.edu>> schrieb am Fr. 27. März 2020 um 15:32:
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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____________________________________
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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____________________________________
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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