FreeSurfer experts, I am trying to mark points on a surface in tksurfer, then obtain their original voxel coordinates. These are some of the problems I have encountered, and some of the instructions and examples I do not yet understand. -Jeff
From: Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> Date: Thursday, January 3, 2013 6:27 PM To: Jeff Eriksen <eriksenj@ohsu.edumailto:eriksenj@ohsu.edu> Subject: Re: [Freesurfer] FW: how to obtain MRI coordinates of scalp surface points marked in tksurfer
Can you cc the list so others can answer? Freeview can rotate....
On Jan 3, 2013, at 8:06 PM, Jeff Eriksen <eriksenj@ohsu.edumailto:eriksenj@ohsu.edu> wrote:
Bruce,
This is what I get when I try to use tksurfer to open the scalp surface created with mkseghead:
********************************************************************************************* kje-macbook:mri jefferiksen$ tksurfer AIRC0001 lh seghead subject is AIRC0001 hemi is lh surface is seghead surfer: current subjects dir: /Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001/mri Reading image info (/Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001) Reading /Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001/mri/orig.mgz surfer: Reading header info from /Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001/mri/orig.mgz ltMNIreadEx: could not open file /Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001/mri/transforms/talairach.xfm No such file or directory surfer: Talairach xform file not found (ignored) surfer: vertices=219128, faces=442484 MRISreadVertexPosition(/Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001/surf/lh.orig): could not open file /Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001/surf/lh.orig No such file or directory MRISreadOriginalProperties: could not read surface file /Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001/surf/lh.orig No such file or directory surfer: single buffered window surfer: tkoInitWindow(AIRC0001) surfer: using interface /Applications/freesurfer/lib/tcl/tksurfer.tcl Reading /Applications/freesurfer/lib/tcl/tkm_common.tcl Reading /Applications/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /Applications/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /Applications/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... mrisReadTriangleFile(/Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001/surf/lh.white): surface doesn't match /Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001/surf/lh.seghead
mrisReadTriangleFile failed. ***********************************************************************************************
The surface displays, but when I click on a point it puts all 0.0s in the Vertex RAS fields. I presume this is because I have not specified a volume or transform.
I am confused by the example given below which uses orig.mgz. I tried to substitute T1.mgz, but it still tries to use orig.mgz above.
*********************************************************************************************** 1. I have a point on the surface and want to compute the CRS for voxel in the orig.mgz that corresponds to this point: VoxCRS = inv(Torig)*[tkrR tkrA tkrS 1]' where [tkrR tkrA tkrS] is the "Vertex RAS" as seen in the tksurfer Tools window (also output of mris_convert). Torig is the Vox2tkrRAS matrix obtained from "mri_info --vox2ras-tkr orig.mgz" (note: this is the same for all orig volumes). Test: click on a point in tksurfer. Use "Vertex RAS" to compute Vox2CRS. Round Vox2CRS to the nearest integer. Hit Save Point in tksurfer. In tkmedit, Goto Saved Point. Compare VoxCRS to "Volume Index". Note: you may need to use the "Volume RAS" from tkmedit in the computation above to get an exact match ************************************************************************************************ I tried mri_info --vox2ras-tkr T1.mgz and got a matrix, which I could use in Matlab to transform, but not without knowing the vertex RAS coordinates.
Have I confused you enough?
From: Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> Date: Wednesday, January 2, 2013 7:08 PM To: Jeff Eriksen <eriksenj@ohsu.edumailto:eriksenj@ohsu.edu> Cc: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: how to obtain MRI coordinates of scalp surface points marked in tksurfer
Hi Jeff The coordinate conversions are documented on our wiki. Or you could do the marking in tkmedit or freeview which will show you voxel and surface RAS coords. There might also be an option to view them in tksurfer too, I can't remember (view->information or something like that) Cheers Bruce
On Jan 2, 2013, at 7:43 PM, Jeff Eriksen <eriksenj@ohsu.edumailto:eriksenj@ohsu.edu> wrote:
HI,
I created a scalp surface mesh with mkheadsurf. I need to mark or select some scalp surface points and obtain their MRI coordinates. That is, if my MRI is 256-cubed I need the (ix,iy,iz) MRI voxel coordinates closest to the scalp mesh point I mark, where these run from 1 to 256 (or 0-255 if you must). The tksurfer display shows several types of floating point coordinates, but they assume an origin in the center of the head somewhere. If I knew the MRI coordinates of this origin I could calculate the original MRI.
Thanks, -Jeff
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tksurfer may be putting all 0s in the RAS field because the head surface does not match the cortical surface (tksurfer is very inflexible in this way). One way around it is to find the vertex number, then find the RAS for that vertex by converting the surface to ascii. freeview might do a better job than tksurfer.
doug
On 01/03/2013 10:38 PM, Jeff Eriksen wrote:
FreeSurfer experts, I am trying to mark points on a surface in tksurfer, then obtain their original voxel coordinates. These are some of the problems I have encountered, and some of the instructions and examples I do not yet understand. -Jeff
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> Date: Thursday, January 3, 2013 6:27 PM To: Jeff Eriksen <eriksenj@ohsu.edu mailto:eriksenj@ohsu.edu> Subject: Re: [Freesurfer] FW: how to obtain MRI coordinates of scalp surface points marked in tksurfer
Can you cc the list so others can answer? Freeview can rotate....
On Jan 3, 2013, at 8:06 PM, Jeff Eriksen <eriksenj@ohsu.edu mailto:eriksenj@ohsu.edu> wrote:
Bruce,
This is what I get when I try to use tksurfer to open the scalp surface created with mkseghead:
kje-macbook:mri jefferiksen$ tksurfer AIRC0001 lh seghead subject is AIRC0001 hemi is lh surface is seghead surfer: current subjects dir: /Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001/mri Reading image info (/Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001) Reading /Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001/mri/orig.mgz surfer: Reading header info from /Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001/mri/orig.mgz ltMNIreadEx: could not open file /Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001/mri/transforms/talairach.xfm No such file or directory surfer: Talairach xform file not found (ignored) surfer: vertices=219128, faces=442484 MRISreadVertexPosition(/Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001/surf/lh.orig): could not open file /Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001/surf/lh.orig No such file or directory MRISreadOriginalProperties: could not read surface file /Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001/surf/lh.orig No such file or directory surfer: single buffered window surfer: tkoInitWindow(AIRC0001) surfer: using interface /Applications/freesurfer/lib/tcl/tksurfer.tcl Reading /Applications/freesurfer/lib/tcl/tkm_common.tcl Reading /Applications/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /Applications/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /Applications/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... mrisReadTriangleFile(/Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001/surf/lh.white): surface doesn't match /Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001/surf/lh.seghead
mrisReadTriangleFile failed.
The surface displays, but when I click on a point it puts all 0.0s in the Vertex RAS fields. I presume this is because I have not specified a volume or transform.
I am confused by the example given below which uses orig.mgz. I tried to substitute T1.mgz, but it still tries to use orig.mgz above.
- I have a point on the surface and want to compute the CRS for
voxel in the orig.mgz that corresponds to this point:
VoxCRS = inv(Torig)*[tkrR tkrA tkrS 1]'
where [tkrR tkrA tkrS] is the "Vertex RAS" as seen in the tksurfer Tools window (also output of mris_convert). Torig is the Vox2tkrRAS matrix obtained from "mri_info --vox2ras-tkr orig.mgz" (note: this is the same for all orig volumes).
Test: click on a point in tksurfer. Use "Vertex RAS" to compute Vox2CRS. Round Vox2CRS to the nearest integer. Hit Save Point in tksurfer. In tkmedit, Goto Saved Point. Compare VoxCRS to "Volume Index". Note: you may need to use the "Volume RAS" from tkmedit in the computation above to get an exact match
I tried mri_info --vox2ras-tkr T1.mgz and got a matrix, which I could use in Matlab to transform, but not without knowing the vertex RAS coordinates.
Have I confused you enough?
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> Date: Wednesday, January 2, 2013 7:08 PM To: Jeff Eriksen <eriksenj@ohsu.edu mailto:eriksenj@ohsu.edu> Cc: "freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: how to obtain MRI coordinates of scalp surface points marked in tksurfer
Hi Jeff The coordinate conversions are documented on our wiki. Or you could do the marking in tkmedit or freeview which will show you voxel and surface RAS coords. There might also be an option to view them in tksurfer too, I can't remember (view->information or something like that) Cheers Bruce
On Jan 2, 2013, at 7:43 PM, Jeff Eriksen <eriksenj@ohsu.edu mailto:eriksenj@ohsu.edu> wrote:
HI,
I created a scalp surface mesh with mkheadsurf. I need to mark or select some scalp surface points and obtain their MRI coordinates. That is, if my MRI is 256-cubed I need the (ix,iy,iz) MRI voxel coordinates closest to the scalp mesh point I mark, where these run from 1 to 256 (or 0-255 if you must). The tksurfer display shows several types of floating point coordinates, but they assume an origin in the center of the head somewhere. If I knew the MRI coordinates of this origin I could calculate the original MRI.
Thanks, -Jeff
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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.
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Douglas N Greve -
Jeff Eriksen