External Email - Use Caution
Dear Freesurfer experts,
I'm trying to convert a volumetric atlas (MICCAI_2012) in NIFTI format to a surface annotation using mris_sample_parc and I would like to kindly ask for your support. I ran recon-all on the corresponding template brain (which I will refer to as ICBM2009 with subject ID "fs_DBS_ICBM2009_T1_1mm"). I also created a custom color LUT called "MICCAI_2012_freesurfer.txt".
However when I run the command mris_sample_parc -ct MICCAI_2012_freesurfer.txt fs_DBS_T1_1mm lh MICCAI_2012.nii MICCAI_2012.annot
and check the results in Freeview, the result is very bad: most of the hemisphere is labelled as the 3rd ventricle, and other labels are completely off as well. To me it looks like it's got something to do with the orientation of either the NIFTI atlas or the white matter surface.
Not sure if this relevant but the NIFTI atlas has RAS orientation and has no Qform matrix (the Sform is present and Sform code is "Scanner Anatomical").
Could you please help me with this?
Thank you very much in advance.
Best regards