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 >>>>>>> >>
-- 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
