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Hello Freesurfer Developers,
I'm trying to get superior colliculus' ROI mannually by freeview. I load "orig.mgz" as volumes and set the "orig.mgz" as the ROI's template then draw the ROI and save it as a label file. After that I use "mri_label2vol --label sc.label --temp T1.nii --reg register.dat --o sc.nii", "T1.nii" is my initial structure image, "register.dat" got from the code:" tkregister2 --mov T1.nii --s SUB --regheader --noedit --reg register.dat", and it worked, but the coordinate mismatch, much different from the SC's position in the T1 space( Load T1.nii as volume and SC.label as ROI in freeview, and they are matched). Can anyone help me? Thank you!
1)FreeSurfer version: freesurfer-local-build-dev-20191104 2)platform: Ubuntu 18.04
I'm not sure what the problem is. You say that they match when you load the T1 and the sc. If so, what is the problem?
On 11/27/2019 7:57 AM, zorothustra wrote:
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Hello Freesurfer Developers,
I'm trying to get superior colliculus' ROI mannually by freeview. I load "orig.mgz" as volumes and set the "orig.mgz" as the ROI's template then draw the ROI and save it as a label file. After that I use "mri_label2vol --label sc.label --temp T1.nii --reg register.dat --o sc.nii", "T1.nii" is my initial structure image, "register.dat" got from the code:" tkregister2 --mov T1.nii --s SUB --regheader --noedit --reg register.dat", and it worked, but the coordinate mismatch, much different from the SC's position in the T1 space( Load T1.nii as volume and SC.label as ROI in freeview, and they are matched). Can anyone help me? Thank you!
1)FreeSurfer version: freesurfer-local-build-dev-20191104 2)platform: Ubuntu 18.04
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Thanks for your reply and sorry to bother you again. The problem is that the volume converted from label which drew by freeview does not match T1. Happy Thanksgiving day!
发件人: Greve, Douglas N.,Ph.D. 发送时间: 2019年11月28日 0:59 收件人: freesurfer@nmr.mgh.harvard.edu 主题: Re: [Freesurfer] Converting labels drew by freeview to volumeError: coordinate mismatch
I'm not sure what the problem is. You say that they match when you load the T1 and the sc. If so, what is the problem? On 11/27/2019 7:57 AM, zorothustra wrote: External Email - Use Caution Hello Freesurfer Developers,
I'm trying to get superior colliculus' ROI mannually by freeview. I load "orig.mgz" as volumes and set the "orig.mgz" as the ROI's template then draw the ROI and save it as a label file. After that I use "mri_label2vol --label sc.label --temp T1.nii --reg register.dat --o sc.nii", "T1.nii" is my initial structure image, "register.dat" got from the code:" tkregister2 --mov T1.nii --s SUB --regheader --noedit --reg register.dat", and it worked, but the coordinate mismatch, much different from the SC's position in the T1 space( Load T1.nii as volume and SC.label as ROI in freeview, and they are matched). Can anyone help me? Thank you!
1)FreeSurfer version: freesurfer-local-build-dev-20191104 2)platform: Ubuntu 18.04
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Try adding --invertmtx to the mri_label2vol command
On 11/28/2019 4:35 AM, Zoro wrote:
External Email - Use Caution Thanks for your reply and sorry to bother you again. The problem is that the volume converted from label which drew by freeview does not match T1. Happy Thanksgiving day!
发件人: Greve, Douglas N.,Ph.D.mailto:DGREVE@mgh.harvard.edu 发送时间: 2019年11月28日 0:59 收件人: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu 主题: Re: [Freesurfer] Converting labels drew by freeview to volumeError: coordinate mismatch
I'm not sure what the problem is. You say that they match when you load the T1 and the sc. If so, what is the problem? On 11/27/2019 7:57 AM, zorothustra wrote:
External Email - Use Caution Hello Freesurfer Developers,
I'm trying to get superior colliculus' ROI mannually by freeview. I load "orig.mgz" as volumes and set the "orig.mgz" as the ROI's template then draw the ROI and save it as a label file. After that I use "mri_label2vol --label sc.label --temp T1.nii --reg register.dat --o sc.nii", "T1.nii" is my initial structure image, "register.dat" got from the code:" tkregister2 --mov T1.nii --s SUB --regheader --noedit --reg register.dat", and it worked, but the coordinate mismatch, much different from the SC's position in the T1 space( Load T1.nii as volume and SC.label as ROI in freeview, and they are matched). Can anyone help me? Thank you!
1)FreeSurfer version: freesurfer-local-build-dev-20191104 2)platform: Ubuntu 18.04
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_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi Douglas, Thanks for your reply! I tried, but the volume and T1 still don't align.
my purpose: make a mask of superior colliculus
Here is how I did: 1) tkregister2 --mov T1.nii --s sub01 --regheader --noedit --reg register.dat 2) open freeview and load orig.mgz→ New ROI and select orig.mgz as the template volume→ draw ROI of superior colliculus slice by slice and save it as sc.label 3) mri_label2vol --label sc.label --temp T1.nii --reg register.dat --o sc.nii --invertmtx
The problem: sc.nii and T1.nii don't align, the ROI of superior colliculus are in the wrong place.
I would highly appreciate If you have any suggestions as the ways to get superior colliculus' ROI or mask.
At 2019-12-03 00:02:15, "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu wrote: Try adding --invertmtx to the mri_label2vol command
On 11/28/2019 4:35 AM, Zoro wrote:
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Thanks for your reply and sorry to bother you again. The problem is that the volume converted from label which drew by freeview does not match T1.
Happy Thanksgiving day!
发件人: Greve, Douglas N.,Ph.D. 发送时间: 2019年11月28日 0:59 收件人: freesurfer@nmr.mgh.harvard.edu 主题: Re: [Freesurfer] Converting labels drew by freeview to volumeError: coordinate mismatch
I'm not sure what the problem is. You say that they match when you load the T1 and the sc. If so, what is the problem?
On 11/27/2019 7:57 AM, zorothustra wrote:
External Email - Use Caution
Hello Freesurfer Developers,
I'm trying to get superior colliculus' ROI mannually by freeview. I load "orig.mgz" as volumes and set the "orig.mgz" as the ROI's template then draw the ROI and save it as a label file. After that I use "mri_label2vol --label sc.label --temp T1.nii --reg register.dat --o sc.nii", "T1.nii" is my initial structure image, "register.dat" got from the code:" tkregister2 --mov T1.nii --s SUB --regheader --noedit --reg register.dat", and it worked, but the coordinate mismatch, much different from the SC's position in the T1 space( Load T1.nii as volume and SC.label as ROI in freeview, and they are matched).
Can anyone help me? Thank you!
1)FreeSurfer version: freesurfer-local-build-dev-20191104
2)platform: Ubuntu 18.04
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
This is actually a problem with mri_label2vol. I have fixed it and put a new copy here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_label2vol run it like this
mri_label2vol --label sc.label --temp T1.nii --reg register.dat --o sc.nii --tkr-template orig.mgz
On 12/3/19 8:23 AM, ZORO wrote:
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Hi Douglas, Thanks for your reply! I tried, but the volume and T1 still don't align.
my purpose: make a mask of superior colliculus
Here is how I did:
- tkregister2 --mov T1.nii --s sub01 --regheader --noedit --reg
register.dat 2) open freeview and load orig.mgz→ New ROI and select orig.mgz as the template volume→ draw ROI of superior colliculus slice by slice and save it as sc.label 3) mri_label2vol --label sc.label --temp T1.nii --reg register.dat --o sc.nii --invertmtx
The problem: sc.nii and T1.nii don't align, the ROI of superior colliculus are in the wrong place.
I would highly appreciate If you have any suggestions as the ways to get superior colliculus' ROI or mask.
At 2019-12-03 00:02:15, "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu wrote:
Try adding --invertmtx to the mri_label2vol command On 11/28/2019 4:35 AM, Zoro wrote:External Email - Use Caution Thanks for your reply and sorry to bother you again. The problem is that the volume converted from label which drew by freeview does not match T1. Happy Thanksgiving day! *发件人**: *Greve, Douglas N.,Ph.D. <mailto:DGREVE@mgh.harvard.edu> *发送时间**: *2019年11月28日0:59 *收件人**: *freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> *主题**: *Re: [Freesurfer] Converting labels drew by freeview to volumeError: coordinate mismatch I'm not sure what the problem is. You say that they match when you load the T1 and the sc. If so, what is the problem? On 11/27/2019 7:57 AM, zorothustra wrote: * External Email - Use Caution * Hello Freesurfer Developers, I'm trying to get superior colliculus' ROI mannually by freeview. I load "orig.mgz" as volumes and set the "orig.mgz" as the ROI's template then draw the ROI and save it as a label file. After that I use "mri_label2vol --label sc.label --temp T1.nii --reg register.dat --o sc.nii", "T1.nii" is my initial structure image, "register.dat" got from the code:" tkregister2 --mov T1.nii --s SUB --regheader --noedit --reg register.dat", and it worked, but the coordinate mismatch, much different from the SC's position in the T1 space( Load T1.nii as volume and SC.label as ROI in freeview, and they are matched). Can anyone help me? Thank you! 1)FreeSurfer version: freesurfer-local-build-dev-20191104 2)platform: Ubuntu 18.04 _______________________________________________ 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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