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Hi there Freesurfer,

I am currently using freesurfer to take DTI metrics (FA, MD) from hippocampal subfields. 

At this point of my exploration with freesurfer, I am able to correctly register the hippocampal subfields and diffusion data, and obtain my FA values from the subfields. However, this is at the individual subject level. 

I will eventually need to register all of my samples in the same space for me to do a group analysis. However I am unsure what the order of registration should be for this process to be feasible. 

Does this order seem feasible for accurate analysis?

1) recon-all all of my subjects 

2) dt_recon all of my subjects (one of the outputs is a registration file, which has registered the DTI data to outputs of recon-all)

3) run the hippocampus segmentation command on all subjects (segmentHA_T1.sh) to obtain hippocampal subfield segmentation 

4) register the segmentation file to the FA maps (output of dt_recon) using vol2subfield command

5) After creating a subfield-FA map for each subject, spatial normalize the samples onto the same space using mri_vol2vol

Thank you so much for taking the time reading my question. If there is a different method to spatially normalizing my datasets, or if there is a more optimal order of registration, I'd be happy to hear from you.

Thank you, 
M

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