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 >>