Hi FS experts,

I have run a hippocampal analysis with v6.0 including the subfields and am now in the process of running an  addtional analysis using the dev6.0 version for the amygdala and posterior/anterior hippocampal measures. I also want to use the 3D rendered volumes of the hippocampus and amygdala as volume ROI masks for tractography.
1. My diffusion data is registered to my T1 data. Just wondering is it the rawavg.mgz file I need to register the ROI's to?
2. I'm using freeview and 3D rendererd the Hippocampus (203-226) and saved that as a volume. Do I use the mri_vol2vol command to align my roi's to the rawavg image for correctly map onto my T1 native space image because when I try that it seems that the ROI volume image can't be opened. I think I must be missing a step when creating the mask perhaps?
3. If I also wish to generate additional masks from the aseg.mgz, will that be done via the same steps used for the hippocampus or do I need to use the fslmaths <input imgae> -thr LUT number of the subcorical structure -uthr lut number again <output filename> first and then regsiter them to the rawavg.mzg?

Thanks for any guidance which is always greatly appreciated.



Best regards

Erik