13 Jan
2024
13 Jan
'24
12:44 p.m.
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 Caution
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:External Email - Use Caution 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:External Email - Use Caution 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:External Email - Use Caution 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. 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