Dear freesurfers,
when I check my mri_converted data after running (1) using <csurf> I find my data shifted relative to the voxel space center (volume index at [128 128 128]) as can be seen in the attached screenshots. The subsequent generation of the "filled" images leaves the cerebellum always attached. I tried to manually set the cutting planes as described in the FreeSurfer Manual (pp. 32-36) but the whole cerebellum is still connected to the brain and always attributed to the left hemisphere.
In addition to that I think the bert "orig" data set is smoothed, right? In comparison to bert does my data look much more grainy. Do I have to smooth my data first?
Any suggestions in how I can proceed in trying to successfully set the cutting planes are most welcome!
Marcus
(1) mri_convert -ot cor -it siemens_dicom $SUBJECTS_DIR/7481/mri/orig/3D/<some file.ima> $SUBJECTS_DIR/7481/mri/orig/
