Hi doug,
thanks for the tip. I covered the translation from RAS to tailarach, but there is a much larger shift unfortunately.
greetings,
martijn
On 6/9/06, Doug Greve greve@nmr.mgh.harvard.edu wrote:
Where is neurolens getting it's coords? There will be a shift in the surf coords. relative to the orig.mgz. If you run
mri_info orig.mgz
you will see c_{ras} values. Try adding or subtracting these.
doug
martijn van den heuvel wrote:
Hi Doug,
Thanks for your reply. Indeed, I can open the surface in both programs, but there seems to be a shift in a coordinate system. I want to plot fiber tracts in Neurolens as well, so I need to know where I can find the exact (0,0,0) coordinate in the pial surface. Using tksurfer the (0,0,0) coordinate is in the center of the volume (RAS), however that is not the case using NeuroLens. So, I thought that maybe there is a translation applied when loading the surface into tksurfer.
greetings, martijn
On 6/8/06, Doug Greve greve@nmr.mgh.harvard.edu wrote:
Hi Martijn,
we still support COR. I'm at a disadvantage here in that I've not used Neurolens before. I'm not even sure what the problem is. You can show the surfaces in neurolens and in tksurfer, so what's the problem?
doug
martijn van den heuvel wrote: Dear Bruce,
Thanks for your quick reply. I posted this question on the Neurolens-forum as well.
I too think it is just a problem of two different coordinate system. Rick (of the Neurolens forum) mentioned that the pial surface coordinate to world coordinate system is stated in a COR.info file. However, I think that the COR.info file is no longer supported by freesurfer, is this correct? Is there an alternative? Sorry, if my question was not totally clear. I will describe what I did:
I translated my anatomy file to talairach space (only translation, no scaling, resliced it so there is not .mat file ) and used it (in SPM analyse format) as input for the freesurfer-train (recon-all -autorecon1,2,3). The recon-all dev table suggests that freesurfer uses brain.finalsurfs.mgz(same orientation as T1.mgz) as the input for creating the surface pial files. In my original anatomy file the (0,0,0) coordinate is around the center of the brain (in talairach space). As my input anatomy is already in Talairach space orig.mgz is also in talairach space and there is a minimum translation by freesurfer to create T1.mgz (I checked this and indead talairach.xfmis almost a 1 1 1 matrix). If freesurfer uses this as the input for the surface rendering, should not be the (0,0,0) coordinate in the middle of the pial surface? Using tksurfer this is indead the case, however using Neurolens this is not the case, there is a large shift. There is a small shift from talairach coordinate system to RAS system, but my surface rendering has a much larger shift (in my example around 45 mm in the Z-direction).
Maybe this COR.info file is the solution, holding the translation from scanner coordinates <-> RAS, however I don't have an example of this file and therefore do not now what this file looks like and what it does.
Hope you can help me with this problem.
Really appreciate your time.
greetings, martijn
On 6/7/06, Bruce Fischl < fischl@nmr.mgh.harvard.edu > wrote:
I think it's probably just displaying them in different
coordinate
systems. tksurfer displays in an RAS coordinate system in which
(0,0,0)
is essentially the center of the volume, whereas Neurolens is
probably
displaying scanner coordinates. Does it matter to you? Not sure I understand - is it causing you any problems?
Bruce
On Wed, 7 Jun 2006, martijn van den heuvel wrote:
> Dear freesurfer-users, > > I want to plot the freesurfer surface rendering (xxx.pial) in
the
program > Neurolens. Loading the image gives no problem and Neurolens
gives a
> beautiful rendering. However, when loading the pial surface in
tksurfer
I > see a difference between the two renderings. The surface in
tksurfer is
> centered to RAS (0,0,0) , like the T1.mgz image (as it supposed
to do).
Im > trying to figure out what this translation is, but I cannot
find the
answer > on the web, hence this email. Does tksurfer loads in a
translation file
> (except for the talaraich.xfm, I got this translation covered),
or does
it > do a general shift to the RAS centre? Generally, Im looking for
the
> translation matrix from RAS to world coordinates, so I can
apply this
> translation to the surface before loading it in Neurolens. > > I hope someone can help me with this question. > > Yours sincerely, > > Martijn van den Heuvel >
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In order to help us help you, please follow the steps in:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://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
In order to help us help you, please follow the steps in:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting