[Freesurfer] center of pial surface in world coordinates
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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] center of pial surface in world coordinates
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.xfm is 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 < [EMAIL PROTECTED] > 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>> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] center of pial surface in world coordinates
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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] center of pial surface in world coordinates
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.xfm is 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 < [EMAIL PROTECTED] > 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 >> > >> > ___ 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 [EMAIL PROTECTED] 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] center of pial surface in world coordinates
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,martijnOn 6/8/06, Doug Greve <[EMAIL PROTECTED]> 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.xfm is 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 < [EMAIL PROTECTED] > 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 >> > >> > ___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D.MGH-NMR Center[EMAIL PROTECTED] 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] center of pial surface in world coordinates
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 <[EMAIL PROTECTED]>
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.xfm is
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 < [EMAIL PROTECTED]
> 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
>> >
>>
>
___
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
[EMAIL PROTECTED]
Phone Number: 617-724-2358
Fax: 617-726-7422
In order to help us help you, please follow the steps in:
surfer.nmr.m
Re: [Freesurfer] center of pial surface in world coordinates
Hi doug,thanks for the tip. I covered the translation from RAS to tailarach, but there is a much larger shift unfortunately.greetings,martijnOn 6/9/06,
Doug Greve <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]>
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.xfm is
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 < [EMAIL PROTECTED]
> 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
>> >
>>
>
___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/fr
