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