On Fri, Jan 12, 2024 at 3:00 PM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:

Map the diffusion data to the subfield space, eg,
mri_vol2vol --mov fa.nii.gz --reg register.lta --targ subfields.mgz --o fa-in-subfields.mgz
Then run mri_segstats
mri_segstats --ctab-default --i fa-in-subfields.mgz --seg subfields.mgz --sum fa-in-subfields.dat

On 1/12/2024 4:53 PM, Mirsol Choi wrote:

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Hi there,

Is there a way to successfully obtain FA/MD values from the hippocampus subfields?

Thank you,

M

On Fri, Jan 12, 2024 at 2:23 PM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:

I'm not sure what you mean. The subfields are an ROI-based analysis. Are you saying you want to do a voxel-based analysis (without reference to ROIs)?

On 1/9/2024 12:05 PM, Mirsol Choi wrote:

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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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