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
<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:
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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