And what coordinate system are the xyz in? doug ps. Please post questions to the list and not to me personally. Thanks!
On 03/27/2012 04:10 PM, Johnson wrote:
Hi I have the tracts in (x,y,z) format not as an nii file regards JG On 03/27/2012 11:25 AM, Douglas N Greve wrote:
Hi Johnson, try something like this:
mri_label2vol --seg tracts.nii --temp orig.mgz --o tracts-in-fs.nii --regheader tracts.nii
doug
On 03/26/2012 03:29 PM, Johnson wrote:
OK T1 space is the space acquired from the machine, original anatomical space regards JG
On 03/26/2012 2:25 PM, Bruce Fischl wrote:
can you post to the list so others can answer? And can you clarify what you mean by "T1" space?
On Mon, 26 Mar 2012, Johnson wrote:
Hi well, I had to transfer the fiber tracts coordinates from DWI space to T1 space, I used the b0 and the T1 for the registration process, I got the transformation matrix and applied it onto the tracts and they fit very well. Now I want to transform the tracts from T1 space to the freesurfer space, I need to know the transformation matrix that was used during the processing if it was saved in any of the logs thanks Johnson On 03/26/2012 2:09 PM, Bruce Fischl wrote:
Hi Johnson
what T1 did you register to? Most of the ones we generate (T1.mgz, brainmask.mgz, ...) are in a common coordinate system and you shouldn't have to transform from one to another. cheers Bruce
On Mon, 26 Mar 2012, Johnson wrote:
> Hi > Let me re-phrase my question: > I already did registration from DWI to T1, this step is OK. > Now I want to go from T1 to FreeSurfer space (aparc+aseg.mgz > file not > the aparc+aseg-in-rawavg file). I know I have two choices: > 1) do registration using bbregister > 2) since Freesurfer during processing have already done this > step, the > transformation matrix is there somewhere, the question is where to > find > it? which log or which file? this choice is better since it is more > accurate. > > Thanks > JG > > On 03/26/2012 12:41 PM, Anastasia Yendiki wrote: >> If you want to register your DWI to T1, you should register to >> mri/brain.mgz. You can do this with bbregister, or with any affine >> registration tool of your choice. >> >> On Mon, 26 Mar 2012, Johnson wrote: >> >>> Hi >>> I found it in a 256x256x256 space while the T1 we use is in >>> different >>> space, I found this page on the registration step: >>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat >>> I wish to know how this script work? >>> >>> mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o >>> aseg-in-rawavg.mgz >>> --regheader aseg.mgz >>> >>> what is the transformation used ? >>> JG >>> >>> >>> On 03/26/2012 12:24 PM, Anastasia Yendiki wrote: >>>> Hi Johnson - The aparc+aseg.mgz is in the same space as >>>> the T1 >>>> used as >>>> input to freesurfer. >>>> >>>> a.y >>>> >>>> On Mon, 26 Mar 2012, Johnson wrote: >>>> >>>>> Hi FS expert >>>>> I need to know the transformation matrix itself since I >>>>> will do >>>> the> transformation in matlab. >>>>> I successfully transformed white matter fibers >>>>> coordinates to T1 >>>> using> AIR 5.0 from LONI lab. >>>>> They provide a transformation matrix. >>>>> Now I want to transform the coordinates from T1 to >>>>> Freesurfer >>>> space, so >>>>> my question is: what is the transformation matrix that >>>>> relates >>>> the T1 >>>>> which FS have used for parcellation and segmentation >>>>> with the> >>>> aparc+aseg.mgz file? >>>>> I searched the logs but couldn't find such matrix. >>>>> I don't want to do a registration step since it will be >>>>> less >>>> accurate> than the one that was generated during the >>>> segmentation >>>> process. >>>>> Also is it just one transformation or a combination of >>>> transformations? >>>>>> 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
They are in the same coordinate system as the original T1 file supplied to FS to generate the aparc+aseg file JG On 03/27/2012 4:41 PM, Douglas N Greve wrote:
And what coordinate system are the xyz in? doug ps. Please post questions to the list and not to me personally. Thanks!
On 03/27/2012 04:10 PM, Johnson wrote:
Hi I have the tracts in (x,y,z) format not as an nii file regards JG On 03/27/2012 11:25 AM, Douglas N Greve wrote:
Hi Johnson, try something like this:
mri_label2vol --seg tracts.nii --temp orig.mgz --o tracts-in-fs.nii --regheader tracts.nii
doug
On 03/26/2012 03:29 PM, Johnson wrote:
OK T1 space is the space acquired from the machine, original anatomical space regards JG
On 03/26/2012 2:25 PM, Bruce Fischl wrote:
can you post to the list so others can answer? And can you clarify what you mean by "T1" space?
On Mon, 26 Mar 2012, Johnson wrote:
Hi well, I had to transfer the fiber tracts coordinates from DWI space to T1 space, I used the b0 and the T1 for the registration process, I got the transformation matrix and applied it onto the tracts and they fit very well. Now I want to transform the tracts from T1 space to the freesurfer space, I need to know the transformation matrix that was used during the processing if it was saved in any of the logs thanks Johnson On 03/26/2012 2:09 PM, Bruce Fischl wrote: > Hi Johnson > > what T1 did you register to? Most of the ones we generate (T1.mgz, > brainmask.mgz, ...) are in a common coordinate system and you > shouldn't > have to transform from one to another. > cheers > Bruce > > > On Mon, 26 Mar 2012, Johnson wrote: > >> Hi >> Let me re-phrase my question: >> I already did registration from DWI to T1, this step is OK. >> Now I want to go from T1 to FreeSurfer space (aparc+aseg.mgz >> file not >> the aparc+aseg-in-rawavg file). I know I have two choices: >> 1) do registration using bbregister >> 2) since Freesurfer during processing have already done this >> step, the >> transformation matrix is there somewhere, the question is where to >> find >> it? which log or which file? this choice is better since it is more >> accurate. >> >> Thanks >> JG >> >> On 03/26/2012 12:41 PM, Anastasia Yendiki wrote: >>> If you want to register your DWI to T1, you should register to >>> mri/brain.mgz. You can do this with bbregister, or with any affine >>> registration tool of your choice. >>> >>> On Mon, 26 Mar 2012, Johnson wrote: >>> >>>> Hi >>>> I found it in a 256x256x256 space while the T1 we use is in >>>> different >>>> space, I found this page on the registration step: >>>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat >>>> I wish to know how this script work? >>>> >>>> mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o >>>> aseg-in-rawavg.mgz >>>> --regheader aseg.mgz >>>> >>>> what is the transformation used ? >>>> JG >>>> >>>> >>>> On 03/26/2012 12:24 PM, Anastasia Yendiki wrote: >>>>> Hi Johnson - The aparc+aseg.mgz is in the same space as >>>>> the T1 >>>>> used as >>>>> input to freesurfer. >>>>> >>>>> a.y >>>>> >>>>> On Mon, 26 Mar 2012, Johnson wrote: >>>>> >>>>>> Hi FS expert >>>>>> I need to know the transformation matrix itself since I >>>>>> will do >>>>> the> transformation in matlab. >>>>>> I successfully transformed white matter fibers >>>>>> coordinates to T1 >>>>> using> AIR 5.0 from LONI lab. >>>>>> They provide a transformation matrix. >>>>>> Now I want to transform the coordinates from T1 to >>>>>> Freesurfer >>>>> space, so >>>>>> my question is: what is the transformation matrix that >>>>>> relates >>>>> the T1 >>>>>> which FS have used for parcellation and segmentation >>>>>> with the> >>>>> aparc+aseg.mgz file? >>>>>> I searched the logs but couldn't find such matrix. >>>>>> I don't want to do a registration step since it will be >>>>>> less >>>>> accurate> than the one that was generated during the >>>>> segmentation >>>>> process. >>>>>> Also is it just one transformation or a combination of >>>>> transformations? >>>>>>> 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 >
Hi Johnson, can you be more specific? scanner coordinates? voxel coordinates?
On 03/27/2012 06:20 PM, Johnson wrote:
They are in the same coordinate system as the original T1 file supplied to FS to generate the aparc+aseg file JG On 03/27/2012 4:41 PM, Douglas N Greve wrote:
And what coordinate system are the xyz in? doug ps. Please post questions to the list and not to me personally. Thanks!
On 03/27/2012 04:10 PM, Johnson wrote:
Hi I have the tracts in (x,y,z) format not as an nii file regards JG On 03/27/2012 11:25 AM, Douglas N Greve wrote:
Hi Johnson, try something like this:
mri_label2vol --seg tracts.nii --temp orig.mgz --o tracts-in-fs.nii --regheader tracts.nii
doug
On 03/26/2012 03:29 PM, Johnson wrote:
OK T1 space is the space acquired from the machine, original anatomical space regards JG
On 03/26/2012 2:25 PM, Bruce Fischl wrote:
can you post to the list so others can answer? And can you clarify what you mean by "T1" space?
On Mon, 26 Mar 2012, Johnson wrote:
> Hi > well, I had to transfer the fiber tracts coordinates from DWI space > to T1 space, I used the b0 and the T1 for the registration > process, I > got the transformation matrix and applied it onto the tracts and > they > fit very well. > Now I want to transform the tracts from T1 space to the freesurfer > space, I need to know the transformation matrix that was used > during > the processing if it was saved in any of the logs > thanks > Johnson > On 03/26/2012 2:09 PM, Bruce Fischl wrote: >> Hi Johnson >> >> what T1 did you register to? Most of the ones we generate (T1.mgz, >> brainmask.mgz, ...) are in a common coordinate system and you >> shouldn't >> have to transform from one to another. >> cheers >> Bruce >> >> >> On Mon, 26 Mar 2012, Johnson wrote: >> >>> Hi >>> Let me re-phrase my question: >>> I already did registration from DWI to T1, this step is OK. >>> Now I want to go from T1 to FreeSurfer space (aparc+aseg.mgz >>> file not >>> the aparc+aseg-in-rawavg file). I know I have two choices: >>> 1) do registration using bbregister >>> 2) since Freesurfer during processing have already done this >>> step, the >>> transformation matrix is there somewhere, the question is >>> where to >>> find >>> it? which log or which file? this choice is better since it is >>> more >>> accurate. >>> >>> Thanks >>> JG >>> >>> On 03/26/2012 12:41 PM, Anastasia Yendiki wrote: >>>> If you want to register your DWI to T1, you should register to >>>> mri/brain.mgz. You can do this with bbregister, or with any >>>> affine >>>> registration tool of your choice. >>>> >>>> On Mon, 26 Mar 2012, Johnson wrote: >>>> >>>>> Hi >>>>> I found it in a 256x256x256 space while the T1 we use is in >>>>> different >>>>> space, I found this page on the registration step: >>>>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat >>>>> I wish to know how this script work? >>>>> >>>>> mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o >>>>> aseg-in-rawavg.mgz >>>>> --regheader aseg.mgz >>>>> >>>>> what is the transformation used ? >>>>> JG >>>>> >>>>> >>>>> On 03/26/2012 12:24 PM, Anastasia Yendiki wrote: >>>>>> Hi Johnson - The aparc+aseg.mgz is in the same space as >>>>>> the T1 >>>>>> used as >>>>>> input to freesurfer. >>>>>> >>>>>> a.y >>>>>> >>>>>> On Mon, 26 Mar 2012, Johnson wrote: >>>>>> >>>>>>> Hi FS expert >>>>>>> I need to know the transformation matrix itself since I >>>>>>> will do >>>>>> the> transformation in matlab. >>>>>>> I successfully transformed white matter fibers >>>>>>> coordinates to T1 >>>>>> using> AIR 5.0 from LONI lab. >>>>>>> They provide a transformation matrix. >>>>>>> Now I want to transform the coordinates from T1 to >>>>>>> Freesurfer >>>>>> space, so >>>>>>> my question is: what is the transformation matrix that >>>>>>> relates >>>>>> the T1 >>>>>>> which FS have used for parcellation and segmentation >>>>>>> with the> >>>>>> aparc+aseg.mgz file? >>>>>>> I searched the logs but couldn't find such matrix. >>>>>>> I don't want to do a registration step since it will be >>>>>>> less >>>>>> accurate> than the one that was generated during the >>>>>> segmentation >>>>>> process. >>>>>>> Also is it just one transformation or a combination of >>>>>> transformations? >>>>>>>> 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 >>
from my understanding, scanner coordinates (i.e. considering the resolution of each voxel) regards JG
On 03/27/2012 6:14 PM, Douglas N Greve wrote:
Hi Johnson, can you be more specific? scanner coordinates? voxel coordinates?
On 03/27/2012 06:20 PM, Johnson wrote:
They are in the same coordinate system as the original T1 file supplied to FS to generate the aparc+aseg file JG On 03/27/2012 4:41 PM, Douglas N Greve wrote:
And what coordinate system are the xyz in? doug ps. Please post questions to the list and not to me personally. Thanks!
On 03/27/2012 04:10 PM, Johnson wrote:
Hi I have the tracts in (x,y,z) format not as an nii file regards JG On 03/27/2012 11:25 AM, Douglas N Greve wrote:
Hi Johnson, try something like this:
mri_label2vol --seg tracts.nii --temp orig.mgz --o tracts-in-fs.nii --regheader tracts.nii
doug
On 03/26/2012 03:29 PM, Johnson wrote:
OK T1 space is the space acquired from the machine, original anatomical space regards JG
On 03/26/2012 2:25 PM, Bruce Fischl wrote: > can you post to the list so others can answer? And can you clarify > what you mean by "T1" space? > > On Mon, 26 Mar 2012, Johnson wrote: > >> Hi >> well, I had to transfer the fiber tracts coordinates from DWI space >> to T1 space, I used the b0 and the T1 for the registration >> process, I >> got the transformation matrix and applied it onto the tracts and >> they >> fit very well. >> Now I want to transform the tracts from T1 space to the freesurfer >> space, I need to know the transformation matrix that was used >> during >> the processing if it was saved in any of the logs >> thanks >> Johnson >> On 03/26/2012 2:09 PM, Bruce Fischl wrote: >>> Hi Johnson >>> >>> what T1 did you register to? Most of the ones we generate (T1.mgz, >>> brainmask.mgz, ...) are in a common coordinate system and you >>> shouldn't >>> have to transform from one to another. >>> cheers >>> Bruce >>> >>> >>> On Mon, 26 Mar 2012, Johnson wrote: >>> >>>> Hi >>>> Let me re-phrase my question: >>>> I already did registration from DWI to T1, this step is OK. >>>> Now I want to go from T1 to FreeSurfer space (aparc+aseg.mgz >>>> file not >>>> the aparc+aseg-in-rawavg file). I know I have two choices: >>>> 1) do registration using bbregister >>>> 2) since Freesurfer during processing have already done this >>>> step, the >>>> transformation matrix is there somewhere, the question is >>>> where to >>>> find >>>> it? which log or which file? this choice is better since it is >>>> more >>>> accurate. >>>> >>>> Thanks >>>> JG >>>> >>>> On 03/26/2012 12:41 PM, Anastasia Yendiki wrote: >>>>> If you want to register your DWI to T1, you should register to >>>>> mri/brain.mgz. You can do this with bbregister, or with any >>>>> affine >>>>> registration tool of your choice. >>>>> >>>>> On Mon, 26 Mar 2012, Johnson wrote: >>>>> >>>>>> Hi >>>>>> I found it in a 256x256x256 space while the T1 we use is in >>>>>> different >>>>>> space, I found this page on the registration step: >>>>>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat >>>>>> I wish to know how this script work? >>>>>> >>>>>> mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o >>>>>> aseg-in-rawavg.mgz >>>>>> --regheader aseg.mgz >>>>>> >>>>>> what is the transformation used ? >>>>>> JG >>>>>> >>>>>> >>>>>> On 03/26/2012 12:24 PM, Anastasia Yendiki wrote: >>>>>>> Hi Johnson - The aparc+aseg.mgz is in the same space as >>>>>>> the T1 >>>>>>> used as >>>>>>> input to freesurfer. >>>>>>> >>>>>>> a.y >>>>>>> >>>>>>> On Mon, 26 Mar 2012, Johnson wrote: >>>>>>> >>>>>>>> Hi FS expert >>>>>>>> I need to know the transformation matrix itself since I >>>>>>>> will do >>>>>>> the> transformation in matlab. >>>>>>>> I successfully transformed white matter fibers >>>>>>>> coordinates to T1 >>>>>>> using> AIR 5.0 from LONI lab. >>>>>>>> They provide a transformation matrix. >>>>>>>> Now I want to transform the coordinates from T1 to >>>>>>>> Freesurfer >>>>>>> space, so >>>>>>>> my question is: what is the transformation matrix that >>>>>>>> relates >>>>>>> the T1 >>>>>>>> which FS have used for parcellation and segmentation >>>>>>>> with the> >>>>>>> aparc+aseg.mgz file? >>>>>>>> I searched the logs but couldn't find such matrix. >>>>>>>> I don't want to do a registration step since it will be >>>>>>>> less >>>>>>> accurate> than the one that was generated during the >>>>>>> segmentation >>>>>>> process. >>>>>>>> Also is it just one transformation or a combination of >>>>>>> transformations? >>>>>>>>> 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 >>>
That might be scanner coordinates or it might be that they just took into account the voxel size but used some other coordinate system. Can you find out exactly what the coordinate system is? I really need that information before I can give you an answer. doug
On 03/27/2012 07:58 PM, Johnson wrote:
from my understanding, scanner coordinates (i.e. considering the resolution of each voxel) regards JG
On 03/27/2012 6:14 PM, Douglas N Greve wrote:
Hi Johnson, can you be more specific? scanner coordinates? voxel coordinates?
On 03/27/2012 06:20 PM, Johnson wrote:
They are in the same coordinate system as the original T1 file supplied to FS to generate the aparc+aseg file JG On 03/27/2012 4:41 PM, Douglas N Greve wrote:
And what coordinate system are the xyz in? doug ps. Please post questions to the list and not to me personally. Thanks!
On 03/27/2012 04:10 PM, Johnson wrote:
Hi I have the tracts in (x,y,z) format not as an nii file regards JG On 03/27/2012 11:25 AM, Douglas N Greve wrote:
Hi Johnson, try something like this:
mri_label2vol --seg tracts.nii --temp orig.mgz --o tracts-in-fs.nii --regheader tracts.nii
doug
On 03/26/2012 03:29 PM, Johnson wrote: > OK > T1 space is the space acquired from the machine, original anatomical > space > regards > JG > > On 03/26/2012 2:25 PM, Bruce Fischl wrote: >> can you post to the list so others can answer? And can you clarify >> what you mean by "T1" space? >> >> On Mon, 26 Mar 2012, Johnson wrote: >> >>> Hi >>> well, I had to transfer the fiber tracts coordinates from DWI space >>> to T1 space, I used the b0 and the T1 for the registration >>> process, I >>> got the transformation matrix and applied it onto the tracts and >>> they >>> fit very well. >>> Now I want to transform the tracts from T1 space to the freesurfer >>> space, I need to know the transformation matrix that was used >>> during >>> the processing if it was saved in any of the logs >>> thanks >>> Johnson >>> On 03/26/2012 2:09 PM, Bruce Fischl wrote: >>>> Hi Johnson >>>> >>>> what T1 did you register to? Most of the ones we generate (T1.mgz, >>>> brainmask.mgz, ...) are in a common coordinate system and you >>>> shouldn't >>>> have to transform from one to another. >>>> cheers >>>> Bruce >>>> >>>> >>>> On Mon, 26 Mar 2012, Johnson wrote: >>>> >>>>> Hi >>>>> Let me re-phrase my question: >>>>> I already did registration from DWI to T1, this step is OK. >>>>> Now I want to go from T1 to FreeSurfer space (aparc+aseg.mgz >>>>> file not >>>>> the aparc+aseg-in-rawavg file). I know I have two choices: >>>>> 1) do registration using bbregister >>>>> 2) since Freesurfer during processing have already done this >>>>> step, the >>>>> transformation matrix is there somewhere, the question is >>>>> where to >>>>> find >>>>> it? which log or which file? this choice is better since it is >>>>> more >>>>> accurate. >>>>> >>>>> Thanks >>>>> JG >>>>> >>>>> On 03/26/2012 12:41 PM, Anastasia Yendiki wrote: >>>>>> If you want to register your DWI to T1, you should register to >>>>>> mri/brain.mgz. You can do this with bbregister, or with any >>>>>> affine >>>>>> registration tool of your choice. >>>>>> >>>>>> On Mon, 26 Mar 2012, Johnson wrote: >>>>>> >>>>>>> Hi >>>>>>> I found it in a 256x256x256 space while the T1 we use is in >>>>>>> different >>>>>>> space, I found this page on the registration step: >>>>>>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat >>>>>>> I wish to know how this script work? >>>>>>> >>>>>>> mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o >>>>>>> aseg-in-rawavg.mgz >>>>>>> --regheader aseg.mgz >>>>>>> >>>>>>> what is the transformation used ? >>>>>>> JG >>>>>>> >>>>>>> >>>>>>> On 03/26/2012 12:24 PM, Anastasia Yendiki wrote: >>>>>>>> Hi Johnson - The aparc+aseg.mgz is in the same space as >>>>>>>> the T1 >>>>>>>> used as >>>>>>>> input to freesurfer. >>>>>>>> >>>>>>>> a.y >>>>>>>> >>>>>>>> On Mon, 26 Mar 2012, Johnson wrote: >>>>>>>> >>>>>>>>> Hi FS expert >>>>>>>>> I need to know the transformation matrix itself since I >>>>>>>>> will do >>>>>>>> the> transformation in matlab. >>>>>>>>> I successfully transformed white matter fibers >>>>>>>>> coordinates to T1 >>>>>>>> using> AIR 5.0 from LONI lab. >>>>>>>>> They provide a transformation matrix. >>>>>>>>> Now I want to transform the coordinates from T1 to >>>>>>>>> Freesurfer >>>>>>>> space, so >>>>>>>>> my question is: what is the transformation matrix that >>>>>>>>> relates >>>>>>>> the T1 >>>>>>>>> which FS have used for parcellation and segmentation >>>>>>>>> with the> >>>>>>>> aparc+aseg.mgz file? >>>>>>>>> I searched the logs but couldn't find such matrix. >>>>>>>>> I don't want to do a registration step since it will be >>>>>>>>> less >>>>>>>> accurate> than the one that was generated during the >>>>>>>> segmentation >>>>>>>> process. >>>>>>>>> Also is it just one transformation or a combination of >>>>>>>> transformations? >>>>>>>>>> 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@nmr.mgh.harvard.edu
-
Douglas N Greve -
Johnson