If I run recon-all with both a T1 and a T2 scan and switch t2pial, does mri_info -tkr2scanner give me the transform to the T1 scanner frame of reference?
And if I run recon-all with many T1's , what does mri_info -tkr2scanner give me then?
Thanks - Don
-tkr2scanner gives the transform that takes "tkregister RAS" and converts it to scanner RAS. "tkregisterRAS" is the RAS system used by surfaces (it, a vertex xyz is in tkregisterRAS). See http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
On 11/10/2016 09:33 PM, Krieger, Donald N. wrote:
If I run recon-all with both a T1 and a T2 scan and switch t2pial, does mri_info –tkr2scanner give me the transform to the T1 scanner frame of reference?
And if I run recon-all with many T1’s , what does mri_info –tkr2scanner give me then?
Thanks - Don
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks for getting back, Doug. I understand - but if there are two scans, aren't there two scanner RAS's since the head presumably moved at least a little from one to the other or the scans could have been done on different scanners?
Don
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, November 11, 2016 3:22 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_info --tkr2scanner result for run with multiple input scans
-tkr2scanner gives the transform that takes "tkregister RAS" and converts it to scanner RAS. "tkregisterRAS" is the RAS system used by surfaces (it, a vertex xyz is in tkregisterRAS). See http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
On 11/10/2016 09:33 PM, Krieger, Donald N. wrote:
If I run recon-all with both a T1 and a T2 scan and switch t2pial, does mri_info –tkr2scanner give me the transform to the T1 scanner frame of reference?
And if I run recon-all with many T1’s , what does mri_info –tkr2scanner give me then?
Thanks - Don
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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If the head has not moved, then they will share a scanner RAS, ie, a given scanner RAS will be at the same place in the head in the two scans, though they will map to different col,row,slice in their respective volumes. If the head has moved, then you will need to perform a registration to get them aligned.
On 11/11/2016 04:17 PM, Krieger, Donald N. wrote:
Thanks for getting back, Doug. I understand - but if there are two scans, aren't there two scanner RAS's since the head presumably moved at least a little from one to the other or the scans could have been done on different scanners?
Don
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, November 11, 2016 3:22 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_info --tkr2scanner result for run with multiple input scans
-tkr2scanner gives the transform that takes "tkregister RAS" and converts it to scanner RAS. "tkregisterRAS" is the RAS system used by surfaces (it, a vertex xyz is in tkregisterRAS). See http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
On 11/10/2016 09:33 PM, Krieger, Donald N. wrote:
If I run recon-all with both a T1 and a T2 scan and switch t2pial, does mri_info –tkr2scanner give me the transform to the T1 scanner frame of reference?
And if I run recon-all with many T1’s , what does mri_info –tkr2scanner give me then?
Thanks - Don
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Now I don't understand.
Here's the situation: Someone has given me a bunch of MEG's with freesurfer runs which were run using both a T1 and a T2 scan with -T2pial . Mri_info --tkr2scanner gives the same transform for aparac+aseg.mgz, T1.mgz, and T2.mgz . I will be coregistering the MEG which comes with each T1/T2 pair . Since I'm getting the same transform from all the .mgz's, I speculated that freesurfer transformed both scans to tkr coordinates, did its thing, and then picked the T1 to provide the tkr2scanner transform. ???
Don
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer- bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Friday, November 11, 2016 4:35 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_info --tkr2scanner result for run with multiple input scans
If the head has not moved, then they will share a scanner RAS, ie, a given scanner RAS will be at the same place in the head in the two scans, though they will map to different col,row,slice in their respective volumes. If the head has moved, then you will need to perform a registration to get them aligned.
On 11/11/2016 04:17 PM, Krieger, Donald N. wrote:
Thanks for getting back, Doug. I understand - but if there are two scans, aren't there two scanner RAS's since
the head presumably moved at least a little from one to the other or the scans could have been done on different scanners?
Don
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, November 11, 2016 3:22 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_info --tkr2scanner result for run with multiple input scans
-tkr2scanner gives the transform that takes "tkregister RAS" and converts it to scanner RAS. "tkregisterRAS" is the RAS system used by surfaces (it, a vertex xyz is in tkregisterRAS). See http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
On 11/10/2016 09:33 PM, Krieger, Donald N. wrote:
If I run recon-all with both a T1 and a T2 scan and switch t2pial, does mri_info -tkr2scanner give me the transform to the T1 scanner frame of reference?
And if I run recon-all with many T1's , what does mri_info -tkr2scanner give me then?
Thanks - Don
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I guess I'm not sure what the problem is. If you need to go from a surface coordinate to scanner coord, then get the tkr2scanner matrix and multiply it by the surface coord. The volumes are not transformed to tkr coords. The various xform matrices are kept with the volume. What are you trying to do?
On 11/11/2016 04:59 PM, Krieger, Donald N. wrote:
Now I don't understand.
Here's the situation: Someone has given me a bunch of MEG's with freesurfer runs which were run using both a T1 and a T2 scan with -T2pial . Mri_info --tkr2scanner gives the same transform for aparac+aseg.mgz, T1.mgz, and T2.mgz . I will be coregistering the MEG which comes with each T1/T2 pair . Since I'm getting the same transform from all the .mgz's, I speculated that freesurfer transformed both scans to tkr coordinates, did its thing, and then picked the T1 to provide the tkr2scanner transform. ???
Don
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer- bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Friday, November 11, 2016 4:35 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_info --tkr2scanner result for run with multiple input scans
If the head has not moved, then they will share a scanner RAS, ie, a given scanner RAS will be at the same place in the head in the two scans, though they will map to different col,row,slice in their respective volumes. If the head has moved, then you will need to perform a registration to get them aligned.
On 11/11/2016 04:17 PM, Krieger, Donald N. wrote:
Thanks for getting back, Doug. I understand - but if there are two scans, aren't there two scanner RAS's since
the head presumably moved at least a little from one to the other or the scans could have been done on different scanners?
Don
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, November 11, 2016 3:22 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_info --tkr2scanner result for run with multiple input scans
-tkr2scanner gives the transform that takes "tkregister RAS" and converts it to scanner RAS. "tkregisterRAS" is the RAS system used by surfaces (it, a vertex xyz is in tkregisterRAS). See http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
On 11/10/2016 09:33 PM, Krieger, Donald N. wrote:
If I run recon-all with both a T1 and a T2 scan and switch t2pial, does mri_info -tkr2scanner give me the transform to the T1 scanner frame of reference?
And if I run recon-all with many T1's , what does mri_info -tkr2scanner give me then?
Thanks - Don
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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
freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve -
Krieger, Donald N.