I am trying to recon a sagittal T1 series from a functional scan, originally in AFNI format. I converted it to COR using mri_convert -it brik /path/to/<file>.BRIK $SUBJECTS_DIR/subjid/mri/orig
The first run of recon-all -stage1 (-nomotioncor) exited with errors (mri_fill exited with non-zero status). It said that the cerebellum may be attached and then had messages related to rh and lh wm seed points so I ran recon-all with -cc-xyz, -rh-xyz, -lh-xyz and -pons-xyz. That finished without errors. When I tried csurf after that, the wm was mainly in the cerebellum, not a whole lot anywhere else.
I was advised to check the T1 to make sure the T1 wm intensities were close to 110. Those intensities are close to 110.
Any idea what might be wrong with this data or with my processing? Thank you for your help, Michele