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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:
External Email - Use CautionHello,
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:
External Email - Use CautionHi 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:
External Email - Use CautionHi 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:
External Email - Use CautionHi 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?
- recon-all all of my subjects
- 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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