External Email - Use Caution
Dear Freesurfer experts,
I have a manual segmentation of a certain brain feature done in Freeview. I want to pool these segmentations from different subjects to create some kind of a heat map/probability map.
In order to do this, I assume I need to convert my segmentation to a volume first (In my case the Talairach space); hence, I tried:
mri_label2vol --seg example.mgz --temp talairach.xfm --o seg_talairach --reg example_orig.mgz
the example_orig.mgz would correspond to the original T1 which I used to do the segmentation.
But this gives me the error message:
ERROR: could not determine type of talairach.xfm
ERROR: reading talairach.xfm header
Where is the problem?
Many thanks!
/Ben
in this case, I might try mri_vol2vol, something like mri_vol2vol --fstal 1 --interp nearest --mov example.mgz --s subject --regheader --o example.mni305.mgz That is a linear transform. If you want a non-linear, I can walk you through that too
On 12/18/19 10:13 AM, Benjamin Ineichen wrote:
External Email - Use Caution
Dear Freesurfer experts,
I have a manual segmentation of a certain brain feature done in Freeview. I want to pool these segmentations from different subjects to create some kind of a heat map/probability map.
In order to do this, I assume I need to convert my segmentation to a volume first (In my case the Talairach space); hence, I tried:
mri_label2vol --seg example.mgz --temp talairach.xfm --o seg_talairach --reg example_orig.mgz
the example_orig.mgz would correspond to the original T1 which I used to do the segmentation.
But this gives me the error message:
ERROR: could not determine type of talairach.xfm
ERROR: reading talairach.xfm header
Where is the problem?
Many thanks!
/Ben
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Many thanks for your quick reply!
I tried your suggestion. I got the error fstal unknown. So I tried talres 1 instead of fstal 1:
mri_vol2vol --talres 1 --interp nearest --mov example.mgz --s 001.mgz --regheader --o example.mni305.mgz but got the error that I need to supply a target volume. adding the flag -targ talairach.xfm did not work. How can I add the Talaraich space as target volume for my manual segmentation example.mgz?
Many thanks!
/Ben
Am Mi., 18. Dez. 2019 um 20:19 Uhr schrieb Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu>:
in this case, I might try mri_vol2vol, something like mri_vol2vol --fstal 1 --interp nearest --mov example.mgz --s subject --regheader --o example.mni305.mgz That is a linear transform. If you want a non-linear, I can walk you through that too
On 12/18/19 10:13 AM, Benjamin Ineichen wrote:
External Email - Use CautionDear Freesurfer experts,
I have a manual segmentation of a certain brain feature done in Freeview. I want to pool these segmentations from different subjects to create some kind of a heat map/probability map.
In order to do this, I assume I need to convert my segmentation to a volume first (In my case the Talairach space); hence, I tried:
mri_label2vol --seg example.mgz --temp talairach.xfm --o seg_talairach --reg example_orig.mgz
the example_orig.mgz would correspond to the original T1 which I used to do the segmentation.
But this gives me the error message:
ERROR: could not determine type of talairach.xfm
ERROR: reading talairach.xfm header
Where is the problem?
Many thanks!
/Ben
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
Use $FREESURFER_HOME/subjects/fsaverage/mri/orig.mgz as the target when you are using the 1mm (there is a mri2.mm folder for 2mm)
On 12/19/2019 11:34 AM, Benjamin Ineichen wrote:
External Email - Use Caution
Many thanks for your quick reply!
I tried your suggestion. I got the error fstal unknown. So I tried talres 1 instead of fstal 1:
mri_vol2vol --talres 1 --interp nearest --mov example.mgz --s 001.mgz --regheader --o example.mni305.mgz
but got the error that I need to supply a target volume. adding the flag -targ talairach.xfm did not work. How can I add the Talaraich space as target volume for my manual segmentation example.mgz?
Many thanks!
/Ben
Am Mi., 18. Dez. 2019 um 20:19 Uhr schrieb Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu>: in this case, I might try mri_vol2vol, something like mri_vol2vol --fstal 1 --interp nearest --mov example.mgz --s subject --regheader --o example.mni305.mgz That is a linear transform. If you want a non-linear, I can walk you through that too
On 12/18/19 10:13 AM, Benjamin Ineichen wrote:
External Email - Use CautionDear Freesurfer experts,
I have a manual segmentation of a certain brain feature done in Freeview. I want to pool these segmentations from different subjects to create some kind of a heat map/probability map.
In order to do this, I assume I need to convert my segmentation to a volume first (In my case the Talairach space); hence, I tried:
mri_label2vol --seg example.mgz --temp talairach.xfm --o seg_talairach --reg example_orig.mgz
the example_orig.mgz would correspond to the original T1 which I used to do the segmentation.
But this gives me the error message:
ERROR: could not determine type of talairach.xfm
ERROR: reading talairach.xfm header
Where is the problem?
Many thanks!
/Ben
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.chmailto: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.chmailto:ineichen@protonmail.ch +41 76 391 04 01
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Benjamin Ineichen -
Greve, Douglas N.,Ph.D.