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 >>>>>>>> >>> > > -- 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
