Hello All,

I have successfully ran the recon-all -all -s subject -hippocampal-subfields-T1 using free surfer v.6 on macOS Sierra.  

In addition to the structural analysis, I want to run resting state functional connectivity analysis using the whole l/r hippocampus as well as specific subfields as structural seeds. I don<t want to generate an average ROI, but generate subject specific HCSF ROIs. 

My understanding is to perform such analysis I need to: 

1)convert the l/rh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz to mni space (MNI152_T1_2mm_brain.nii.gz).

I ran the mni152reg command, however I doubt that the default settings apply to the hippocampal subfields. Is there options I could use to have the subfields register to MNI 2mm space using mni152reg?   

2)Generate .nii rois for the whole and subfield regions of the hippocampus. 

Using mrs_convert I was able to convert the (l/r)h.hippoSfLabels-T1.v10.FSvoxelSpace.mgz to .nii, getting one global hippocampus per hemisphere. Is there a way to automatically generate subfields ROIs?

Thank you,

Annie