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The amygdala nuclei labels from segmentHA_T1.sh seem to behave differently in standard freesurfer registration commands than other labels from aparc+aseg.mgz: I can't get the amygdala nuclei to register to my functional space correctly despite no issues with aparc+aseg labels. Are additional steps needed to correct header or orientation information when using amygdala nuclei labels? I'm extracting labels from one of the amygdala FSVoxelSpace files.
Below is an example of the command I use to extract labels + register to functional space that isn't working. These commands work great with labels from aparc+aseg.mgz but end up in completely incorrect positions for any of the segmentHA-T1 amygdala nuclei. There is no error message, the issue is just that the output masks are in the wrong location.
mri_extract_label rh.hippoAmygLabels.HBT.FSvoxelSpace.mgz 7001 labels/nuclei1_rh.nii
mri_vol2vol --mov myfunc --targ labels/nuclei1_rh.nii --reg func2anat.dat --inv --o nuclei1_funcspace.nii
The label file from the extract label command looks correct when overlaid on the anatomical. The issue seems to arise after vol2vol command -- the output mask is in the wrong area (eg amygdala nuclei are in the cerebellumafter vol2vol). The same vol2vol command works fine with the whole amygdala label from aparc+aseg, + I have checked the registration .dat file from bbregister is correct.
Any advice would be appreciated! I've checked the header information using fslhd and the orientations from masks that worked (aparc+aseg) and didn't work (rh.hippoAmygLabels) appear identical.
*I've abbreviated the name of the input to mri_extract_label command for simplification, the full name is: rh.hippoAmygLabels-T1.v22.HBT.FSvoxelSpace.mgz