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
<dgr...@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.
Thank you,
M
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