Hi,
I have been working with an image dataset of EPI images and MR images that have been registered in the freesurfer (transformation for which is stored in a .reg file).
A T1 mgz volume was made using the following command: mri_convert -it analyze -ot mgh -i T1001.img -o T1.mgz
I formed the EPI volume using the following command: mri_convert -it analyze -ot mgh -i F0001.img -o BH1.mgz
when I load the T1 volume, and then overlay the EPI volume in tkmedit, with the reg file for transformation, I get a yellow box superimposed over a T1 image. The EPI volume itself appears to be properly formed, as I can read it directly into freesurfer and get a properly formed image. Was wondering if anyone had any suggestions as to what may be going wrong?
Thanks,
Salil Soman sal@bwh.harvard.edu