Bruce,

This is what I get when I try to use tksurfer to open the scalp surface created with mkseghead:

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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.

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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.

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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

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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>
Date: Wednesday, January 2, 2013 7:08 PM
To: Jeff Eriksen <eriksenj@ohsu.edu>
Cc: "freesurfer@nmr.mgh.harvard.edu" <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> 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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