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 >>>>>> >>>>> > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
