Hi Can someone tell me please in*_details_*what does this line do? mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz --regheader aseg.mgz thanks
Hi Johnson
I believe it resamples the aseg to have the same geometry as the original scan.
cheers Bruce On Wed, 11 Apr 2012, Johnson wrote:
Hi Can someone tell me please in details what does this line do? mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz --reg header aseg.mgz thanks
And it exactly does that, does it register them together or use a pre-known transformation matrix On 04/11/2012 3:46 PM, Bruce Fischl wrote:
Hi Johnson
I believe it resamples the aseg to have the same geometry as the original scan.
cheers Bruce On Wed, 11 Apr 2012, Johnson wrote:
Hi Can someone tell me please in details what does this line do? mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz --reg header aseg.mgz thanks
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.
it registers them based on the header information, but since the aseg is derived from the rawavg that should be exactly correct
On Wed, 11 Apr 2012, Johnson wrote:
And it exactly does that, does it register them together or use a pre-known transformation matrix On 04/11/2012 3:46 PM, Bruce Fischl wrote:
Hi Johnson
I believe it resamples the aseg to have the same geometry as the original scan.
cheers Bruce On Wed, 11 Apr 2012, Johnson wrote:
Hi Can someone tell me please in details what does this line do? mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz --reg header aseg.mgz thanks
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.
great, so if I can read the header from the aseg file and the header from the rawavg header file I would be able to transfer any point from the aseg space to the rawavg space is that correct ?
On 04/11/2012 4:40 PM, Bruce Fischl wrote:
it registers them based on the header information, but since the aseg is derived from the rawavg that should be exactly correct
On Wed, 11 Apr 2012, Johnson wrote:
And it exactly does that, does it register them together or use a pre-known transformation matrix On 04/11/2012 3:46 PM, Bruce Fischl wrote:
Hi Johnson
I believe it resamples the aseg to have the same geometry as the original scan.
cheers Bruce On Wed, 11 Apr 2012, Johnson wrote:
Hi Can someone tell me please in details what does this line do? mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz --reg header aseg.mgz thanks
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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Yes, that is correct.
On 04/11/2012 06:54 PM, Johnson wrote:
great, so if I can read the header from the aseg file and the header from the rawavg header file I would be able to transfer any point from the aseg space to the rawavg space is that correct ?
On 04/11/2012 4:40 PM, Bruce Fischl wrote:
it registers them based on the header information, but since the aseg is derived from the rawavg that should be exactly correct
On Wed, 11 Apr 2012, Johnson wrote:
And it exactly does that, does it register them together or use a pre-known transformation matrix On 04/11/2012 3:46 PM, Bruce Fischl wrote:
Hi Johnson
I believe it resamples the aseg to have the same geometry as the original scan.
cheers Bruce On Wed, 11 Apr 2012, Johnson wrote:
Hi Can someone tell me please in details what does this line do? mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz --reg header aseg.mgz thanks
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
yes On Wed, 11 Apr 2012, Johnson wrote:
great, so if I can read the header from the aseg file and the header from the rawavg header file I would be able to transfer any point from the aseg space to the rawavg space is that correct ?
On 04/11/2012 4:40 PM, Bruce Fischl wrote:
it registers them based on the header information, but since the aseg is derived from the rawavg that should be exactly correct
On Wed, 11 Apr 2012, Johnson wrote:
And it exactly does that, does it register them together or use a pre-known transformation matrix On 04/11/2012 3:46 PM, Bruce Fischl wrote:
Hi Johnson
I believe it resamples the aseg to have the same geometry as the original scan.
cheers Bruce On Wed, 11 Apr 2012, Johnson wrote:
Hi Can someone tell me please in details what does this line do? mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz --reg header aseg.mgz thanks
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
there are two transformation matrices one in aseg and one in rawavg, how do I use them ?
On 04/11/2012 6:12 PM, Bruce Fischl wrote:
yes On Wed, 11 Apr 2012, Johnson wrote:
great, so if I can read the header from the aseg file and the header from the rawavg header file I would be able to transfer any point from the aseg space to the rawavg space is that correct ?
On 04/11/2012 4:40 PM, Bruce Fischl wrote:
it registers them based on the header information, but since the aseg is derived from the rawavg that should be exactly correct
On Wed, 11 Apr 2012, Johnson wrote:
And it exactly does that, does it register them together or use a pre-known transformation matrix On 04/11/2012 3:46 PM, Bruce Fischl wrote:
Hi Johnson
I believe it resamples the aseg to have the same geometry as the original scan.
cheers Bruce On Wed, 11 Apr 2012, Johnson wrote:
Hi Can someone tell me please in details what does this line do? mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz --reg header aseg.mgz thanks
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
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Invert one and compose it with the other
On Apr 11, 2012, at 7:48 PM, Johnson jgadel2@uic.edu wrote:
there are two transformation matrices one in aseg and one in rawavg, how do I use them ?
On 04/11/2012 6:12 PM, Bruce Fischl wrote:
yes On Wed, 11 Apr 2012, Johnson wrote:
great, so if I can read the header from the aseg file and the header from the rawavg header file I would be able to transfer any point from the aseg space to the rawavg space is that correct ?
On 04/11/2012 4:40 PM, Bruce Fischl wrote:
it registers them based on the header information, but since the aseg is derived from the rawavg that should be exactly correct
On Wed, 11 Apr 2012, Johnson wrote:
And it exactly does that, does it register them together or use a pre-known transformation matrix On 04/11/2012 3:46 PM, Bruce Fischl wrote:
Hi Johnson
I believe it resamples the aseg to have the same geometry as the original scan.
cheers Bruce On Wed, 11 Apr 2012, Johnson wrote:
> Hi > Can someone tell me please in details what does this line do? > mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz > --reg > header aseg.mgz > thanks > > 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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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Johnson J. GadElkarim Research Assistant, Department Of Psychiatry, PhD Candidate, Department Of Electrical& Computer Eng., University Of Illinois at Chicago Mob: 312 - 376 - 7322 Email: jgadel2@uic.edu
so to be clear about it, suppose T1 is the matrix in aseg and T2 is the one in rawavg, to transform from aseg to rawavg I will apply invert(T1)*T2 is that correct?
On 4/11/2012 8:12 PM, Bruce Fischl wrote:
Invert one and compose it with the other
On Apr 11, 2012, at 7:48 PM, Johnsonjgadel2@uic.edu wrote:
there are two transformation matrices one in aseg and one in rawavg, how do I use them ?
On 04/11/2012 6:12 PM, Bruce Fischl wrote:
yes On Wed, 11 Apr 2012, Johnson wrote:
great, so if I can read the header from the aseg file and the header from the rawavg header file I would be able to transfer any point from the aseg space to the rawavg space is that correct ?
On 04/11/2012 4:40 PM, Bruce Fischl wrote:
it registers them based on the header information, but since the aseg is derived from the rawavg that should be exactly correct
On Wed, 11 Apr 2012, Johnson wrote:
And it exactly does that, does it register them together or use a pre-known transformation matrix On 04/11/2012 3:46 PM, Bruce Fischl wrote: > Hi Johnson > > I believe it resamples the aseg to have the same geometry as the original > scan. > > cheers > Bruce > On Wed, 11 Apr 2012, Johnson wrote: > >> Hi >> Can someone tell me please in details what does this line do? >> mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz >> --reg >> header aseg.mgz >> thanks >> >> > 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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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Johnson J. GadElkarim Research Assistant, Department Of Psychiatry, PhD Candidate, Department Of Electrical& Computer Eng., University Of Illinois at Chicago Mob: 312 - 376 - 7322 Email: jgadel2@uic.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
so to be clear about it, suppose T1 is the matrix in aseg and T2 is the one in rawavg, to transform from aseg to rawavg I will apply invert(T1)*T2 is that correct?
On 4/11/2012 8:12 PM, Bruce Fischl wrote:
Invert one and compose it with the other
On Apr 11, 2012, at 7:48 PM, Johnsonjgadel2@uic.edu wrote:
there are two transformation matrices one in aseg and one in rawavg, how do I use them ?
On 04/11/2012 6:12 PM, Bruce Fischl wrote:
yes On Wed, 11 Apr 2012, Johnson wrote:
great, so if I can read the header from the aseg file and the header from the rawavg header file I would be able to transfer any point from the aseg space to the rawavg space is that correct ?
On 04/11/2012 4:40 PM, Bruce Fischl wrote:
it registers them based on the header information, but since the aseg is derived from the rawavg that should be exactly correct
On Wed, 11 Apr 2012, Johnson wrote:
> And it exactly does that, does it register them together or use a > pre-known > transformation matrix > On 04/11/2012 3:46 PM, Bruce Fischl wrote: >> Hi Johnson >> >> I believe it resamples the aseg to have the same geometry as the original >> scan. >> >> cheers >> Bruce >> On Wed, 11 Apr 2012, Johnson wrote: >> >>> Hi >>> Can someone tell me please in details what does this line do? >>> mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz >>> --reg >>> header aseg.mgz >>> thanks >>> >>> >> 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Johnson J. GadElkarim Research Assistant, Department Of Psychiatry, PhD Candidate, Department Of Electrical& Computer Eng., University Of Illinois at Chicago Mob: 312 - 376 - 7322 Email: jgadel2@uic.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi Johnson
it depends whether you are using the ras2vox or vox2ras. It should be:
V_rawavg = M_ras2vox_rawavg * inv(M_ras2vox_aseg) * V_aseg
Where the V_* are 4x1 homogenous vectors.
cheers Bruce
On Thu, 12 Apr 2012, Johnson wrote:
so to be clear about it, suppose T1 is the matrix in aseg and T2 is the one in rawavg, to transform from aseg to rawavg I will apply invert(T1)*T2 is that correct?
On 4/11/2012 8:12 PM, Bruce Fischl wrote:
Invert one and compose it with the other
On Apr 11, 2012, at 7:48 PM, Johnsonjgadel2@uic.edu wrote:
there are two transformation matrices one in aseg and one in rawavg, how do I use them ?
On 04/11/2012 6:12 PM, Bruce Fischl wrote:
yes On Wed, 11 Apr 2012, Johnson wrote:
great, so if I can read the header from the aseg file and the header from the rawavg header file I would be able to transfer any point from the aseg space to the rawavg space is that correct ?
On 04/11/2012 4:40 PM, Bruce Fischl wrote: > it registers them based on the header information, but since the aseg > is > derived from the rawavg that should be exactly correct > > > On Wed, 11 Apr 2012, Johnson wrote: > >> And it exactly does that, does it register them together or use a >> pre-known >> transformation matrix >> On 04/11/2012 3:46 PM, Bruce Fischl wrote: >>> Hi Johnson >>> >>> I believe it resamples the aseg to have the same geometry as the >>> original >>> scan. >>> >>> cheers >>> Bruce >>> On Wed, 11 Apr 2012, Johnson wrote: >>> >>>> Hi >>>> Can someone tell me please in details what does this line do? >>>> mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o >>>> aseg-in-rawavg.mgz >>>> --reg >>>> header aseg.mgz >>>> thanks >>>> >>>> >>> 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 >
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-- Johnson J. GadElkarim Research Assistant, Department Of Psychiatry, PhD Candidate, Department Of Electrical& Computer Eng., University Of Illinois at Chicago Mob: 312 - 376 - 7322 Email: jgadel2@uic.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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The vector coordinates will be in the voxel space
On 04/12/2012 11:54 AM, Bruce Fischl wrote:
Hi Johnson
it depends whether you are using the ras2vox or vox2ras. It should be:
V_rawavg = M_ras2vox_rawavg * inv(M_ras2vox_aseg) * V_aseg
Where the V_* are 4x1 homogenous vectors.
cheers Bruce
On Thu, 12 Apr 2012, Johnson wrote:
so to be clear about it, suppose T1 is the matrix in aseg and T2 is the one in rawavg, to transform from aseg to rawavg I will apply invert(T1)*T2 is that correct?
On 4/11/2012 8:12 PM, Bruce Fischl wrote:
Invert one and compose it with the other
On Apr 11, 2012, at 7:48 PM, Johnsonjgadel2@uic.edu wrote:
there are two transformation matrices one in aseg and one in rawavg, how do I use them ?
On 04/11/2012 6:12 PM, Bruce Fischl wrote:
yes On Wed, 11 Apr 2012, Johnson wrote:
> great, so if I can read the header from the aseg file and the header > from the > rawavg header file I would be able to transfer any point from the aseg > space > to the rawavg space is that correct ? > > On 04/11/2012 4:40 PM, Bruce Fischl wrote: >> it registers them based on the header information, but since the aseg >> is >> derived from the rawavg that should be exactly correct >> >> >> On Wed, 11 Apr 2012, Johnson wrote: >> >>> And it exactly does that, does it register them together or use a >>> pre-known >>> transformation matrix >>> On 04/11/2012 3:46 PM, Bruce Fischl wrote: >>>> Hi Johnson >>>> >>>> I believe it resamples the aseg to have the same geometry as the >>>> original >>>> scan. >>>> >>>> cheers >>>> Bruce >>>> On Wed, 11 Apr 2012, Johnson wrote: >>>> >>>>> Hi >>>>> Can someone tell me please in details what does this line do? >>>>> mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o >>>>> aseg-in-rawavg.mgz >>>>> --reg >>>>> header aseg.mgz >>>>> thanks >>>>> >>>>> >>>> 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 >> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Johnson J. GadElkarim Research Assistant, Department Of Psychiatry, PhD Candidate, Department Of Electrical& Computer Eng., University Of Illinois at Chicago Mob: 312 - 376 - 7322 Email: jgadel2@uic.edu
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
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yes On Thu, 12 Apr 2012, Johnson wrote:
The vector coordinates will be in the voxel space
On 04/12/2012 11:54 AM, Bruce Fischl wrote:
Hi Johnson
it depends whether you are using the ras2vox or vox2ras. It should be:
V_rawavg = M_ras2vox_rawavg * inv(M_ras2vox_aseg) * V_aseg
Where the V_* are 4x1 homogenous vectors.
cheers Bruce
On Thu, 12 Apr 2012, Johnson wrote:
so to be clear about it, suppose T1 is the matrix in aseg and T2 is the one in rawavg, to transform from aseg to rawavg I will apply invert(T1)*T2 is that correct?
On 4/11/2012 8:12 PM, Bruce Fischl wrote:
Invert one and compose it with the other
On Apr 11, 2012, at 7:48 PM, Johnsonjgadel2@uic.edu wrote:
there are two transformation matrices one in aseg and one in rawavg, how do I use them ?
On 04/11/2012 6:12 PM, Bruce Fischl wrote: > yes > On Wed, 11 Apr 2012, Johnson wrote: > >> great, so if I can read the header from the aseg file and the header >> from the >> rawavg header file I would be able to transfer any point from the >> aseg >> space >> to the rawavg space is that correct ? >> >> On 04/11/2012 4:40 PM, Bruce Fischl wrote: >>> it registers them based on the header information, but since the >>> aseg >>> is >>> derived from the rawavg that should be exactly correct >>> >>> >>> On Wed, 11 Apr 2012, Johnson wrote: >>> >>>> And it exactly does that, does it register them together or use a >>>> pre-known >>>> transformation matrix >>>> On 04/11/2012 3:46 PM, Bruce Fischl wrote: >>>>> Hi Johnson >>>>> >>>>> I believe it resamples the aseg to have the same geometry as the >>>>> original >>>>> scan. >>>>> >>>>> cheers >>>>> Bruce >>>>> On Wed, 11 Apr 2012, Johnson wrote: >>>>> >>>>>> Hi >>>>>> Can someone tell me please in details what does this line do? >>>>>> mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o >>>>>> aseg-in-rawavg.mgz >>>>>> --reg >>>>>> header aseg.mgz >>>>>> thanks >>>>>> >>>>>> >>>>> 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 >>> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
Johnson J. GadElkarim Research Assistant, Department Of Psychiatry, PhD Candidate, Department Of Electrical& Computer Eng., University Of Illinois at Chicago Mob: 312 - 376 - 7322 Email: jgadel2@uic.edu
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I do the transformation in Matlab, I found out that the matlab *load_mgh* function returns the vox2ras matrix, where can I find the ras2vox matrix?
On 04/12/2012 12:11 PM, Bruce Fischl wrote:
yes On Thu, 12 Apr 2012, Johnson wrote:
The vector coordinates will be in the voxel space
On 04/12/2012 11:54 AM, Bruce Fischl wrote:
Hi Johnson
it depends whether you are using the ras2vox or vox2ras. It should be:
V_rawavg = M_ras2vox_rawavg * inv(M_ras2vox_aseg) * V_aseg
Where the V_* are 4x1 homogenous vectors.
cheers Bruce
On Thu, 12 Apr 2012, Johnson wrote:
so to be clear about it, suppose T1 is the matrix in aseg and T2 is the one in rawavg, to transform from aseg to rawavg I will apply invert(T1)*T2 is that correct?
On 4/11/2012 8:12 PM, Bruce Fischl wrote:
Invert one and compose it with the other
On Apr 11, 2012, at 7:48 PM, Johnsonjgadel2@uic.edu wrote:
> there are two transformation matrices one in aseg and one in rawavg, > how > do I use them ? > > On 04/11/2012 6:12 PM, Bruce Fischl wrote: >> yes >> On Wed, 11 Apr 2012, Johnson wrote: >> >>> great, so if I can read the header from the aseg file and the header >>> from the >>> rawavg header file I would be able to transfer any point from the >>> aseg >>> space >>> to the rawavg space is that correct ? >>> >>> On 04/11/2012 4:40 PM, Bruce Fischl wrote: >>>> it registers them based on the header information, but since the >>>> aseg >>>> is >>>> derived from the rawavg that should be exactly correct >>>> >>>> >>>> On Wed, 11 Apr 2012, Johnson wrote: >>>> >>>>> And it exactly does that, does it register them together or use a >>>>> pre-known >>>>> transformation matrix >>>>> On 04/11/2012 3:46 PM, Bruce Fischl wrote: >>>>>> Hi Johnson >>>>>> >>>>>> I believe it resamples the aseg to have the same geometry as the >>>>>> original >>>>>> scan. >>>>>> >>>>>> cheers >>>>>> Bruce >>>>>> On Wed, 11 Apr 2012, Johnson wrote: >>>>>> >>>>>>> Hi >>>>>>> Can someone tell me please in details what does this line do? >>>>>>> mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o >>>>>>> aseg-in-rawavg.mgz >>>>>>> --reg >>>>>>> header aseg.mgz >>>>>>> thanks >>>>>>> >>>>>>> >>>>>> 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 >>>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > -- > Johnson J. GadElkarim > Research Assistant, Department Of Psychiatry, > PhD Candidate, Department Of Electrical& Computer Eng., > University Of Illinois at Chicago > Mob: 312 - 376 - 7322 > Email: jgadel2@uic.edu > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Take the inverse
On 04/12/2012 01:47 PM, Johnson wrote:
I do the transformation in Matlab, I found out that the matlab *load_mgh* function returns the vox2ras matrix, where can I find the ras2vox matrix?
On 04/12/2012 12:11 PM, Bruce Fischl wrote:
yes On Thu, 12 Apr 2012, Johnson wrote:
The vector coordinates will be in the voxel space
On 04/12/2012 11:54 AM, Bruce Fischl wrote:
Hi Johnson
it depends whether you are using the ras2vox or vox2ras. It should be:
V_rawavg = M_ras2vox_rawavg * inv(M_ras2vox_aseg) * V_aseg
Where the V_* are 4x1 homogenous vectors.
cheers Bruce
On Thu, 12 Apr 2012, Johnson wrote:
so to be clear about it, suppose T1 is the matrix in aseg and T2 is the one in rawavg, to transform from aseg to rawavg I will apply invert(T1)*T2 is that correct?
On 4/11/2012 8:12 PM, Bruce Fischl wrote:
> Invert one and compose it with the other > > > > On Apr 11, 2012, at 7:48 PM, Johnsonjgadel2@uic.edu mailto:jgadel2@uic.edu wrote: > >> there are two transformation matrices one in aseg and one in rawavg, >> how >> do I use them ? >> >> On 04/11/2012 6:12 PM, Bruce Fischl wrote: >>> yes >>> On Wed, 11 Apr 2012, Johnson wrote: >>> >>>> great, so if I can read the header from the aseg file and the header >>>> from the >>>> rawavg header file I would be able to transfer any point from the >>>> aseg >>>> space >>>> to the rawavg space is that correct ? >>>> >>>> On 04/11/2012 4:40 PM, Bruce Fischl wrote: >>>>> it registers them based on the header information, but since the >>>>> aseg >>>>> is >>>>> derived from the rawavg that should be exactly correct >>>>> >>>>> >>>>> On Wed, 11 Apr 2012, Johnson wrote: >>>>> >>>>>> And it exactly does that, does it register them together or use a >>>>>> pre-known >>>>>> transformation matrix >>>>>> On 04/11/2012 3:46 PM, Bruce Fischl wrote: >>>>>>> Hi Johnson >>>>>>> >>>>>>> I believe it resamples the aseg to have the same geometry as the >>>>>>> original >>>>>>> scan. >>>>>>> >>>>>>> cheers >>>>>>> Bruce >>>>>>> On Wed, 11 Apr 2012, Johnson wrote: >>>>>>> >>>>>>>> Hi >>>>>>>> Can someone tell me please in details what does this line do? >>>>>>>> mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o >>>>>>>> aseg-in-rawavg.mgz >>>>>>>> --reg >>>>>>>> header aseg.mgz >>>>>>>> thanks >>>>>>>> >>>>>>>> >>>>>>> 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 mailto:Freesurfer@nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >> -- >> Johnson J. GadElkarim >> Research Assistant, Department Of Psychiatry, >> PhD Candidate, Department Of Electrical& Computer Eng., >> University Of Illinois at Chicago >> Mob: 312 - 376 - 7322 >> Email:jgadel2@uic.edu mailto:jgadel2@uic.edu >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-- Johnson J. GadElkarim Research Assistant, Department Of Psychiatry, PhD Candidate, Department Of Electrical& Computer Eng., University Of Illinois at Chicago Mob: 312 - 376 - 7322 Email:jgadel2@uic.edu mailto:jgadel2@uic.edu
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thanks it works now :) On 04/12/2012 12:48 PM, Douglas N Greve wrote:
Take the inverse
On 04/12/2012 01:47 PM, Johnson wrote:
I do the transformation in Matlab, I found out that the matlab *load_mgh* function returns the vox2ras matrix, where can I find the ras2vox matrix?
On 04/12/2012 12:11 PM, Bruce Fischl wrote:
yes On Thu, 12 Apr 2012, Johnson wrote:
The vector coordinates will be in the voxel space
On 04/12/2012 11:54 AM, Bruce Fischl wrote:
Hi Johnson
it depends whether you are using the ras2vox or vox2ras. It should be:
V_rawavg = M_ras2vox_rawavg * inv(M_ras2vox_aseg) * V_aseg
Where the V_* are 4x1 homogenous vectors.
cheers Bruce
On Thu, 12 Apr 2012, Johnson wrote:
so to be clear about it, suppose T1 is the matrix in aseg and T2 is the one in rawavg, to transform from aseg to rawavg I will apply invert(T1)*T2 is that correct?
On 4/11/2012 8:12 PM, Bruce Fischl wrote: >> Invert one and compose it with the other >> >> >> >> On Apr 11, 2012, at 7:48 PM, Johnsonjgadel2@uic.edu mailto:jgadel2@uic.edu wrote: >> >>> there are two transformation matrices one in aseg and one in rawavg, >>> how >>> do I use them ? >>> >>> On 04/11/2012 6:12 PM, Bruce Fischl wrote: >>>> yes >>>> On Wed, 11 Apr 2012, Johnson wrote: >>>> >>>>> great, so if I can read the header from the aseg file and the header >>>>> from the >>>>> rawavg header file I would be able to transfer any point from the >>>>> aseg >>>>> space >>>>> to the rawavg space is that correct ? >>>>> >>>>> On 04/11/2012 4:40 PM, Bruce Fischl wrote: >>>>>> it registers them based on the header information, but since the >>>>>> aseg >>>>>> is >>>>>> derived from the rawavg that should be exactly correct >>>>>> >>>>>> >>>>>> On Wed, 11 Apr 2012, Johnson wrote: >>>>>> >>>>>>> And it exactly does that, does it register them together or use a >>>>>>> pre-known >>>>>>> transformation matrix >>>>>>> On 04/11/2012 3:46 PM, Bruce Fischl wrote: >>>>>>>> Hi Johnson >>>>>>>> >>>>>>>> I believe it resamples the aseg to have the same geometry as the >>>>>>>> original >>>>>>>> scan. >>>>>>>> >>>>>>>> cheers >>>>>>>> Bruce >>>>>>>> On Wed, 11 Apr 2012, Johnson wrote: >>>>>>>> >>>>>>>>> Hi >>>>>>>>> Can someone tell me please in details what does this line do? >>>>>>>>> mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o >>>>>>>>> aseg-in-rawavg.mgz >>>>>>>>> --reg >>>>>>>>> header aseg.mgz >>>>>>>>> thanks >>>>>>>>> >>>>>>>>> >>>>>>>> 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.edumailto:Freesurfer@nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>> -- >>> Johnson J. GadElkarim >>> Research Assistant, Department Of Psychiatry, >>> PhD Candidate, Department Of Electrical& Computer Eng., >>> University Of Illinois at Chicago >>> Mob: 312 - 376 - 7322 >>> Email:jgadel2@uic.edumailto:jgadel2@uic.edu >>> >>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >
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-- Johnson J. GadElkarim Research Assistant, Department Of Psychiatry, PhD Candidate, Department Of Electrical& Computer Eng., University Of Illinois at Chicago Mob: 312 - 376 - 7322 Email:jgadel2@uic.edumailto:jgadel2@uic.edu
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Douglas N Greve -
Johnson