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 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
<dgr...@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
<dgr...@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
<dgr...@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
<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:
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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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