try this https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
On 5/16/17 12:34 PM, Cong wrote: > Dear Doug > I think my problem may caused by that extracted ROI have different > coordination to original > T1 image, although they match well in freeview. For example, one voxel is > [148,144,131] in > extracted left thalamus but [71,130,89] in original T1.nii and T1.mgz. So how > to extract a ROI having same coordinate > with T1? > > Regards > Cong >> From: Douglas Greve <gr...@nmr.mgh.harvard.edu> >> >> >> no idea. you'll proably have to contact the MRIcro group >> >> >> On 5/16/17 8:28 AM, Cong wrote: >>> Dear FSers >>> I extracted left thalamus as ROI volume from aseg.mgz by this command: >>> / mri_binarize --i control001/mri/aseg.mgz --match 10 --o >>> control001/roi/l_thal.nii/ >>> I overlaid l_thal.nii to control001.nii in MRIcro software in a >>> Macbook and it looks well. >>> However, when I overlaid l_thal.nii to control001.nii in Windows >>> MRIcro, it comes a Warning: >>> this NIFTI image includes an rotation transformation. >>> When I open these two files same time, the left thalamus mismatch >>> obviously to original T1 image. >>> I attached an image to show my problem. I try to register this ROI >>> volume to diffusion B0 image, >>> and the registered left thalamus appears in the same wrong position >>> as shown in attached image. >>> Could someone tell me what?s wrong and how to solve it. >>> >>> Regards >>> Cong > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
