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 >>> >> >> >> > -- 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: jgad...@uic.edu _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
