External Email - Use Caution
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
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 Caution
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 mailto: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 mailto: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
External Email - Use Caution
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:
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
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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
what is "native space"?
On 3/6/2020 12:09 PM, Benjamin Ineichen wrote:
External Email - Use Caution
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 mailto: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 Caution 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 <mailto: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 <mailto:ineichen@protonmail.ch> +41 76 391 04 01 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 mailto: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 mailto: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
External Email - Use Caution
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
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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 listFreesurfer@nmr.mgh.harvard.eduhttps://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
External Email - Use Caution
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:
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
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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 listFreesurfer@nmr.mgh.harvard.eduhttps://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
What do you mean by "the average space of the subjects"?
On 3/24/2020 2:01 PM, Benjamin Ineichen wrote:
External Email - Use Caution
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 mailto: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 <mailto:dgreve@mgh.harvard.edu>>: what is "native space"? On 3/6/2020 12:09 PM, Benjamin Ineichen wrote:External Email - Use Caution 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 <mailto: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 Caution 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 <mailto: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 <mailto:ineichen@protonmail.ch> +41 76 391 04 01 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto: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 <mailto:ineichen@protonmail.ch> +41 76 391 04 01 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto: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 <mailto:ineichen@protonmail.ch> +41 76 391 04 01-- ____________________________________ Benjamin Victor Ineichen, MD PhD Karolinska Institutet Center for Molecular Medicine Stockholm, Sweden ineichen@protonmail.ch mailto: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 mailto: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
External Email - Use Caution
The space i created from all subjects using make_average_subject.
Douglas N. Greve dgreve@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:
External Email - Use CautionDear 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:
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
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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 listFreesurfer@nmr.mgh.harvard.eduhttps://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
-- ____________________________________ 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 listFreesurfer@nmr.mgh.harvard.eduhttps://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
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 <dgreve@mgh.harvard.edu mailto:dgreve@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:External Email - Use Caution 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 <mailto: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 <mailto:dgreve@mgh.harvard.edu>>: what is "native space"? On 3/6/2020 12:09 PM, Benjamin Ineichen wrote:External Email - Use Caution 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 <mailto: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 Caution 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 <mailto: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 <mailto:ineichen@protonmail.ch> +41 76 391 04 01 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto: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 <mailto:ineichen@protonmail.ch> +41 76 391 04 01 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto: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 <mailto:ineichen@protonmail.ch> +41 76 391 04 01 -- ____________________________________ Benjamin Victor Ineichen, MD PhD Karolinska Institutet Center for Molecular Medicine Stockholm, Sweden ineichen@protonmail.ch <mailto: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 <mailto:ineichen@protonmail.ch> +41 76 391 04 01 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 mailto: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 mailto: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
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Thanks, but I want to transform my ROI to the average space from my subjects (as created by make_average_subject). How do i get the xfm file to convert my ROI to this average space?
/Ben
Am Fr., 27. März 2020 um 16:27 Uhr schrieb Douglas N. Greve < dgreve@mgh.harvard.edu>:
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:
External Email - Use CautionThe space i created from all subjects using make_average_subject.
Douglas N. Greve dgreve@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:
External Email - Use CautionDear 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:
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
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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 listFreesurfer@nmr.mgh.harvard.eduhttps://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
-- ____________________________________ 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 listFreesurfer@nmr.mgh.harvard.eduhttps://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 listFreesurfer@nmr.mgh.harvard.eduhttps://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
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