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