Re: [Freesurfer] Sample registration question

Yes, that would be an ROI analysis On 1/13/2024 1:00 PM, Mirsol Choi wrote: External Email - Use Caution 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 wou

Re: [Freesurfer] Sample registration question

External Email - Use Caution Thank you for taking the time to respond on a weekend. On Sat, Jan 13, 2024 at 11:00 AM Mirsol Choi wrote: > Hello, > > My goal is to compare the FA and MD values of hippocampal subfields (only > inside the hippocampus) between cognitively normal, MC

Re: [Freesurfer] Sample registration question

External Email - Use Caution 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 t

Re: [Freesurfer] Sample registration question

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,

Re: [Freesurfer] Sample registration question

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 D

Re: [Freesurfer] Sample registration question

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 fo

Re: [Freesurfer] Sample registration question

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

Re: [Freesurfer] Sample registration question

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

Re: [Freesurfer] Sample registration question

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 wrote: > I'm not sure what you mean. The subfields are an ROI-based analysis. Are > you sayin

Re: [Freesurfer] Sample registration question

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 D

[Freesurfer] Sample registration question

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 F