Dear List, I successfully completed the FS-to-F99 tutorial and now I am trying to reproduce the steps with my own FreeSurfer dataset. According to the FS-to-F99 tutorial, I need to have my mri volume "into LPI orientation" and "the surfaces and volume need to be in register". My original volume is in LIA orientation and is in register with my surface, in the sense that when I open both on FreeSurfer's tkmedit they are well-aligned to each other (I don't know how to check that they are in register otherwise). If I use this surface and volume on FS-to-F99's Stage-1 script and open the resulting spec file with Caret, the volume's axes are wrong and the points on the surface and in the volume don't match (I see this by clicking on the surface and looking what is then highlighted on the volume window). If I transform the volume into LPI orientation (using FreeSurfer's mri_convert command), the new volume has the desired orientation and, interestingly, it is still well-aligned to the surface in FreeSurfer's tkmedit. However, when I use this surface and volume on the FS-toF99's Stage-1 script, the volume and the surface are still not well-aligned, even though the axes labels are now correct. How could I fix things so that my volume and surface are in register when shown in Caret?
Thank you very much, Pablo _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
