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 >