Dear experts,
I am trying to use T2-weighted images (0.5x0.5x1mm) as an additional scan to a T1-weighted image (0.7x0.7x0.7mm) for hippocampal subfield segmentation in Freesurfer 6. The T2-weighted data is a slab which includes the whole hippocampus and its y-axis is parallel to the hippocampal long axis (image dimensions [384,384,50]). When I try to use recon-all -s <subject_name> -hippocampal-subfields-T2 <file name of additional scan> <analysisID>I always get a faulty alignment (through visual inspection by overlaying T2.FSspace.mgz on T1.mgz in freeview or by looking at the quality control image T1_to_T2.v10.QC.gif), even when I manually align the images beforehand.
Do you have any idea or hint how to improve the registration and thus start the segmentation correctly? I also tried to find out which registration tool is used for this (mri_robust_register?) in order to play around with it and would also be thankful for any hint on this.
Thank you for your advice and time,
Best,
Frauke