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Thank you for taking the time to respond on a weekend.

On Sat, Jan 13, 2024 at 11:00 AM Mirsol Choi <mirsol@ualberta.ca> wrote:
Hello,

My goal is to compare the FA and MD values of hippocampal subfields (only inside the hippocampus) between cognitively normal, MCI, and AD subjects. I am unsure if this would require a voxel wise analysis or an ROI analysis… to my understanding this is more of a ROI analysis between subjects - is this assumption incorrect?

Thank you,
Peter 

On Sat, Jan 13, 2024 at 10:44 AM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:
So this is where I get confused on your intentions because you say that you want to do a voxel-wise analysis of an ROI. Do you mean you want to do a voxelwise analysis but only inside, eg, whole hippocampus?

On 1/12/2024 6:07 PM, Mirsol Choi wrote:

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Hello,

Sorry I should have clarified. Yes, I would like to perform voxelwise analysis of FA and MD values of hippocampal subfield between subjects. Is this possible with free surfer?

Thank you again for your time.

M

On Fri, Jan 12, 2024 at 4:05 PM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:
oh, I thought you wanted to do an ROI analysis. You mean for a voxelwise analysis?

On 1/12/2024 5:46 PM, Mirsol Choi wrote:

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Hi there, 


Following the first registration step, should I also run another registration command to put all fa-in-subfields.mgz for each subject onto the same space for inter subject analysis of FA values? 

Thanks again,
M

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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